diff --git a/.test/config/config.yaml b/.test/config/config.yaml
index 5c359dd..0688b17 100644
--- a/.test/config/config.yaml
+++ b/.test/config/config.yaml
@@ -149,14 +149,12 @@ params:
     extra_saf: "" # goes to all -doSaf runs
     extra_beagle: "" # goes to all -doGlf 2 runs
     domajorminor: 1 # Currently only compatible with values 1, 2, 4, 5
-    domaf: 1 # Currently only compatible with values 1, 2, 3
-    popmafmaj: "population" # "all" or "population"
+    domaf: 1
     snp_pval: "1e-6"
     min_maf: -1 # Set -1 to disable
     mindepthind_heterozygosity: 1
   ngsrelate:
-    ibsrelate-only-extra: ""
-    freqbased-extra: ""
+    prune: true
   ngsld:
     max_kb_dist_est-ld: 200
     rnd_sample_est-ld: 0.001
diff --git a/config/config.yaml b/config/config.yaml
index 5b6922f..bd25994 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -148,14 +148,12 @@ params:
     extra_saf: "" # goes to all -doSaf runs
     extra_beagle: "" # goes to all -doGlf 2 runs
     domajorminor: 1 # Currently only compatible with values 1, 2, 4, 5
-    domaf: 1 # Currently only compatible with values 1, 2, 3
-    popmafmaj: "population" # "all" or "population"
+    domaf: 1
     snp_pval: "1e-6"
     min_maf: -1 # Set -1 to disable
     mindepthind_heterozygosity: 1
   ngsrelate:
-    ibsrelate-only-extra: ""
-    freqbased-extra: ""
+    prune: false
   ngsld:
     max_kb_dist_est-ld: 4000
     rnd_sample_est-ld: 0.001
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 6594381..e191e3a 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -59,7 +59,6 @@ wildcard_constraints:
     dp=".{0}|.dp[1-9][0-9]*",
     chunk="[0-9]+",
     sites="|".join(filters),
-    maj="all|pop|anc|ref",
 
 
 # Accumulate desired output files from config file
diff --git a/workflow/rules/3.2_beagles.smk b/workflow/rules/3.2_beagles.smk
index e38aa14..979f9f9 100644
--- a/workflow/rules/3.2_beagles.smk
+++ b/workflow/rules/3.2_beagles.smk
@@ -9,7 +9,7 @@ rule angsd_doGlf2:
     population beagle files, even if a population is fixed for a certain allele.
     """
     input:
-        unpack(get_sitesfile),
+        unpack(filt_depth),
         unpack(get_anc_ref),
         bam="results/datasets/{dataset}/bamlists/{dataset}.{ref}_{population}{dp}.bamlist",
         bams=get_bamlist_bams,
@@ -18,13 +18,13 @@ rule angsd_doGlf2:
         reffai="results/ref/{ref}/{ref}.fa.fai",
         regions="results/datasets/{dataset}/filters/chunks/{ref}_chunk{chunk}.rf",
     output:
-        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.beagle.gz",
-        maf="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.mafs.gz",
-        arg="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.arg",
+        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.beagle.gz",
+        maf="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.mafs.gz",
+        arg="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.arg",
     log:
-        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.log",
+        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.log",
     benchmark:
-        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.log"
+        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.log"
     container:
         angsd_container
     params:
@@ -33,9 +33,10 @@ rule angsd_doGlf2:
         extra_beagle=config["params"]["angsd"]["extra_beagle"],
         mapQ=config["mapQ"],
         baseQ=config["baseQ"],
+        snp_pval=config["params"]["angsd"]["snp_pval"],
         maf=config["params"]["angsd"]["domaf"],
-        snp_pval_maf=get_snppval_maf,
-        majmin=get_majmin,
+        minmaf=config["params"]["angsd"]["min_maf"],
+        majmin=config["params"]["angsd"]["domajorminor"],
         counts=get_docounts,
         trans=get_trans,
         nind=get_nind,
@@ -48,12 +49,12 @@ rule angsd_doGlf2:
     shell:
         """
         angsd -doGlf 2 -bam {input.bam} -GL {params.gl_model} -ref {input.ref} \
-            {params.majmin} -doMaf {params.maf} {params.snp_pval_maf} \
-            -nThreads {threads} {params.extra} -minMapQ {params.mapQ} \
-            -minQ {params.baseQ} -sites {input.sites} -anc {input.anc} \
-            {params.extra_beagle} -rf {input.regions} {params.minind} \
-            -setMinDepthInd {params.mininddp} {params.counts} \
-            -rmTrans {params.trans} -out {params.out} &> {log}
+            -doMajorMinor {params.majmin} -doMaf {params.maf} -minMaf {params.minmaf} \
+            -SNP_pval {params.snp_pval} -nThreads {threads} {params.extra} \
+            -minMapQ {params.mapQ} -minQ {params.baseQ} -sites {input.sites} \
+            -anc {input.anc} {params.extra_beagle} -rf {input.regions} {params.minind} \
+            -setMinDepthInd {params.mininddp} {params.counts} -rmTrans {params.trans} \
+            -out {params.out} &> {log}
         """
 
 
@@ -63,15 +64,15 @@ rule merge_beagle:
     """
     input:
         lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{{maj}}maj.beagle.gz",
+            "results/datasets/{{dataset}}/beagles/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.beagle.gz",
             chunk=chunklist,
         ),
     output:
-        beagle="results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.beagle.gz",
+        beagle="results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.beagle.gz",
     log:
-        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge-beagle.log",
+        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge-beagle.log",
     benchmark:
-        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge-beagle.log"
+        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge-beagle.log"
     container:
         shell_container
     resources:
@@ -93,15 +94,15 @@ rule merge_maf:
     """
     input:
         lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{{maj}}maj.mafs.gz",
+            "results/datasets/{{dataset}}/beagles/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.mafs.gz",
             chunk=chunklist,
         ),
     output:
-        maf="results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.mafs.gz",
+        maf="results/datasets/{dataset}/mafs/{dataset}.{ref}_{population}{dp}_{sites}-filts.mafs.gz",
     log:
-        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge-mafs.log",
+        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge-mafs.log",
     benchmark:
-        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge-mafs.log"
+        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge-mafs.log"
     container:
         shell_container
     resources:
@@ -123,13 +124,13 @@ rule snpset:
     dataset.
     """
     input:
-        "results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.mafs.gz",
+        "results/datasets/{dataset}/mafs/{dataset}.{ref}_{population}{dp}_{sites}-filts.mafs.gz",
     output:
-        "results/datasets/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_snps.sites",
+        "results/datasets/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts_snps.sites",
     log:
-        "logs/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_snps.log",
+        "logs/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts_snps.log",
     benchmark:
-        "benchmarks/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_snps.log"
+        "benchmarks/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts_snps.log"
     container:
         shell_container
     shell:
diff --git a/workflow/rules/4.0_estimate_LD.smk b/workflow/rules/4.0_estimate_LD.smk
index d950c04..5d9f610 100644
--- a/workflow/rules/4.0_estimate_LD.smk
+++ b/workflow/rules/4.0_estimate_LD.smk
@@ -8,19 +8,19 @@ rule ngsLD_estLD:
     Estimates pairwise linkage disequilibrium between SNPs.
     """
     input:
-        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.beagle.gz",
+        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.beagle.gz",
         bamlist="results/datasets/{dataset}/bamlists/{dataset}.{ref}_{population}{dp}.bamlist",
     output:
         ld=temp(
-            "results/datasets/{dataset}/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz"
+            "results/datasets/{dataset}/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz"
         ),
         pos=temp(
-            "results/datasets/{dataset}/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.pos",
+            "results/datasets/{dataset}/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.pos",
         ),
     log:
-        "logs/{dataset}/ngsLD/estLD/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.log",
+        "logs/{dataset}/ngsLD/estLD/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/estLD/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.log"
+        "benchmarks/{dataset}/ngsLD/estLD/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.log"
     container:
         ngsld_container
     threads: lambda wildcards, attempt: attempt
@@ -50,9 +50,8 @@ rule ngsLD_estLD:
 rule combine_LD_files:
     input:
         ldgz=expand(
-            "results/datasets/{{dataset}}/analyses/ngsLD/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{maj}maj.ld_maxkbdist-{{maxkb}}_rndsample-{{rndsmp}}.gz",
+            "results/datasets/{{dataset}}/analyses/ngsLD/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.ld_maxkbdist-{{maxkb}}_rndsample-{{rndsmp}}.gz",
             chunk=chunklist,
-            maj=get_maj,
         ),
     output:
         ldgz="results/datasets/{dataset}/analyses/ngsLD/{dataset}.{ref}_{population}{dp}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz",
diff --git a/workflow/rules/4.1_linkage_pruning.smk b/workflow/rules/4.1_linkage_pruning.smk
index 3230951..975726b 100644
--- a/workflow/rules/4.1_linkage_pruning.smk
+++ b/workflow/rules/4.1_linkage_pruning.smk
@@ -7,13 +7,13 @@ rule ngsLD_prune_sites:
     Prunes SNPs to produce a list of SNPs in linkage equilibrium.
     """
     input:
-        ld="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-1.gz",
+        ld="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-1.gz",
     output:
-        sites="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.sites",
+        sites="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.sites",
     log:
-        "logs/{dataset}/ngsLD/prune_sites/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj_maxkbdist-{maxkb}_minr2-{r2}.log",
+        "logs/{dataset}/ngsLD/prune_sites/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts_maxkbdist-{maxkb}_minr2-{r2}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/prune_sites/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj_maxkbdist-{maxkb}_minr2-{r2}.log"
+        "benchmarks/{dataset}/ngsLD/prune_sites/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts_maxkbdist-{maxkb}_minr2-{r2}.log"
     container:
         ngsld_container
     threads: 4
@@ -36,21 +36,21 @@ rule prune_chunk_beagle:
     Subsets beagle file to pruned SNPs.
     """
     input:
-        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.beagle.gz",
-        sites="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.sites",
+        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.beagle.gz",
+        sites="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.sites",
     output:
-        prunedgz="results/datasets/{dataset}/beagles/pruned/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+        prunedgz="results/datasets/{dataset}/beagles/pruned/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
     log:
-        "logs/{dataset}/ngsLD/prune_beagle/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
+        "logs/{dataset}/ngsLD/prune_beagle/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/prune_beagle/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
+        "benchmarks/{dataset}/ngsLD/prune_beagle/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
     container:
         shell_container
     shadow:
         "minimal"
     threads: lambda wildcards, attempt: attempt
     params:
-        pruned="results/datasets/{dataset}/beagles/pruned/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle",
+        pruned="results/datasets/{dataset}/beagles/pruned/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle",
     resources:
         runtime=lambda wildcards, attempt: attempt * 120,
     shell:
@@ -78,15 +78,15 @@ rule merge_pruned_beagles:
     """
     input:
         pruned=lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/pruned/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{{maj}}maj.pruned_maxkbdist-{{maxkb}}_minr2-{{r2}}.beagle.gz",
+            "results/datasets/{{dataset}}/beagles/pruned/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.pruned_maxkbdist-{{maxkb}}_minr2-{{r2}}.beagle.gz",
             chunk=chunklist,
         ),
     output:
-        beagle="results/datasets/{dataset}/beagles/pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+        beagle="results/datasets/{dataset}/beagles/pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
     log:
-        "logs/{dataset}/ngsLD/merge_pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
+        "logs/{dataset}/ngsLD/merge_pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/merge_pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
+        "benchmarks/{dataset}/ngsLD/merge_pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
     wildcard_constraints:
         population="|".join(
             ["all"]
diff --git a/workflow/rules/4.2_linkage_decay.smk b/workflow/rules/4.2_linkage_decay.smk
index 7cdd98b..49fd718 100644
--- a/workflow/rules/4.2_linkage_decay.smk
+++ b/workflow/rules/4.2_linkage_decay.smk
@@ -1,19 +1,19 @@
 rule combine_LDdecay_files:
     input:
         ldgz=expand(
-            "results/datasets/{{dataset}}/analyses/ngsLD/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{{maj}}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz",
+            "results/datasets/{{dataset}}/analyses/ngsLD/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz",
             chunk=chunklist,
             maxkb=config["params"]["ngsld"]["max_kb_dist_decay"],
             rndsmp=config["params"]["ngsld"]["rnd_sample_decay"],
         ),
     output:
         ldgz=temp(
-            "results/datasets/{dataset}/analyses/ngsLD/decay/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.LDdecay.gz"
+            "results/datasets/{dataset}/analyses/ngsLD/decay/{dataset}.{ref}_{population}{dp}_{sites}-filts.LDdecay.gz"
         ),
     log:
-        "logs/{dataset}/ngsLD/combine_LDdecay_files/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.ld_decay.log",
+        "logs/{dataset}/ngsLD/combine_LDdecay_files/{dataset}.{ref}_{population}{dp}_{sites}-filts.ld_decay.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/combine_LDdecay_files/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.ld_decay.log"
+        "benchmarks/{dataset}/ngsLD/combine_LDdecay_files/{dataset}.{ref}_{population}{dp}_{sites}-filts.ld_decay.log"
     container:
         shell_container
     shell:
@@ -24,10 +24,7 @@ rule combine_LDdecay_files:
 
 rule fit_LD_decay:
     input:
-        lambda w: expand(
-            "results/datasets/{{dataset}}/analyses/ngsLD/decay/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj.LDdecay.gz",
-            maj=get_maj,
-        ),
+        "results/datasets/{dataset}/analyses/ngsLD/decay/{dataset}.{ref}_{population}{dp}_{sites}-filts.LDdecay.gz",
     output:
         plot=report(
             "results/datasets/{dataset}/plots/LD_decay/{dataset}.{ref}_{population}{dp}_{sites}-filts.LDdecay.pdf",
diff --git a/workflow/rules/5.0_relatedness.smk b/workflow/rules/5.0_relatedness.smk
index 56d2d33..0695616 100644
--- a/workflow/rules/5.0_relatedness.smk
+++ b/workflow/rules/5.0_relatedness.smk
@@ -164,10 +164,7 @@ rule ngsrelate_ibsrelate_only:
     does not require allele frequencies.
     """
     input:
-        beagle=lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj.beagle.gz",
-            maj=get_maj,
-        ),
+        unpack(get_ngsrelate_input),
         inds="results/datasets/{dataset}/poplists/{dataset}_{population}{dp}.indiv.list",
     output:
         ngsrelate=temp(
@@ -184,7 +181,6 @@ rule ngsrelate_ibsrelate_only:
     threads: lambda wildcards, attempt: attempt * 4
     params:
         nind=get_nind,
-        extra=config["params"]["ngsrelate"]["ibsrelate-only-extra"],
     resources:
         runtime=lambda wildcards, attempt: attempt * 360,
     shell:
@@ -194,73 +190,43 @@ rule ngsrelate_ibsrelate_only:
         echo $nsites {params.nind}
         cut -f1 {input.inds} | tail -n +2 > {output.samples}
         ngsRelate -G {input.beagle} -n {params.nind} -L $nsites \
-            -O {output.ngsrelate} -z {output.samples} {params.extra}
+            -O {output.relate} -z {output.samples}
         cut -f3-5,30-35 {output.ngsrelate} > {output.ibsrelate}) &> {log}
         """
 
 
-rule ngsrelate_freqbased:
-    """
-    Estimates inbreeding and relatedness measures using NGSrelate. This will use
-    allele frequencies, enabling all coefficients, including IBS relate ones,
-    all will be kept.
-    """
-    input:
-        beagle=lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj.beagle.gz",
-            maj=get_maj,
-        ),
-        mafs=lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj.mafs.gz",
-            maj=get_maj,
-        ),
-        inds="results/datasets/{dataset}/poplists/{dataset}_{population}{dp}.indiv.list",
-    output:
-        relate="results/datasets/{dataset}/analyses/kinship/ngsrelate/{dataset}.{ref}_{population}{dp}_{sites}-filts_ngsrelate-freq.tsv",
-        freq="results/datasets/{dataset}/analyses/kinship/ngsrelate/{dataset}.{ref}_{population}{dp}_{sites}-filts_ngsrelate-freq.freqs",
-        samples="results/datasets/{dataset}/analyses/kinship/ngsrelate/{dataset}.{ref}_{population}{dp}_{sites}-filts_samples.ngsrelate-freq.list",
-    wildcard_constraints:
-        population="|".join(pop_list),
-    log:
-        "logs/{dataset}/kinship/ngsrelate/{dataset}.{ref}_{population}{dp}_{sites}-filts.ngsrelate-freq.log",
-    container:
-        ngsrelate_container
-    threads: lambda wildcards, attempt: attempt * 4
-    params:
-        nind=get_nind,
-        extra=config["params"]["ngsrelate"]["freqbased-extra"],
-    resources:
-        runtime=lambda wildcards, attempt: attempt * 360,
-    shell:
-        r"""
-        (echo "nind"
-        echo {params.nind}
-        cut -f1 {input.inds} | tail -n +2 > {output.samples}
-        zcat {input.mafs} | cut -f7 | sed 1d > {output.freq}
-        ngsRelate -G {input.beagle} -n {params.nind} -O {output.relate} \
-            -z {output.samples} -f {output.freq} {params.extra}) &> {log}
-        """
-
-
-rule ngsrelate_freqbased_merge:
-    input:
-        relates=expand(
-            "results/datasets/{{dataset}}/analyses/kinship/ngsrelate/{{dataset}}.{{ref}}_{population}{{dp}}_{{sites}}-filts_ngsrelate-freq.tsv",
-            population=pop_list,
-        ),
-    output:
-        "results/datasets/{dataset}/analyses/kinship/ngsrelate/{dataset}.{ref}_all{dp}_{sites}-filts_ngsrelate-freq.tsv",
-    log:
-        "logs/{dataset}/kinship/ngsrelate/{dataset}.{ref}_all{dp}_{sites}-filts.ngsrelate-freq.log",
-    container:
-        shell_container
-    shell:
-        """
-        (head -n 1 {input.relates[0]} > {output}
-        for i in {input.relates}; do
-            tail -n+2 $i >> {output}
-        done) 2> {log}
-        """
+# rule ngsrelate_freqbased:
+#     """
+#     Estimates inbreeding and relatedness measures using NGSrelate. This will use
+#     allele frequencies, enabling all coefficients, including IBS relate ones.
+#     All will be kept.
+#     """
+#     input:
+#         unpack(get_ngsrelate_input),
+#         inds="results/datasets/{dataset}/poplists/{dataset}_{population}{dp}.indiv.list",
+#     output:
+#         relate="results/datasets/{dataset}/analyses/kinship/ngsrelate/{dataset}.{ref}_{population}{dp}_{sites}-filts_relate.tsv",
+#         samples="results/datasets/{dataset}/analyses/kinship/ngsrelate/{dataset}.{ref}_{population}{dp}_{sites}-filts_samples.list",
+#     wildcard_constraints:
+#         population="all",
+#     log:
+#         "logs/{dataset}/kinship/ngsrelate/{dataset}.{ref}_{population}{dp}_{sites}-filts.log",
+#     container:
+#         ngsrelate_container
+#     threads: lambda wildcards, attempt: attempt * 4
+#     params:
+#         nind=get_nind,
+#     resources:
+#         runtime=lambda wildcards, attempt: attempt * 360,
+#     shell:
+#         r"""
+#         (nsites=$(zcat {input.beagle} | tail -n +2 | wc -l)
+#         echo "nsites nind"
+#         echo $nsites {params.nind}
+#         cut -f1 {input.inds} | tail -n +2 > {output.samples}
+#         ngsRelate -G {input.beagle} -n {params.nind} -L $nsites -O {output.relate} \
+#             -z {output.samples}) &> {log}
+#         """
 
 
 rule ngsrelate_summary:
@@ -281,8 +247,6 @@ rule ngsrelate_summary:
                 "Type": "Table",
             },
         ),
-    wildcard_constraints:
-        method="ngsrelate-freq|ibsrelate-nofreq",
     log:
         "logs/{dataset}/kinship/ngsrelate/{dataset}.{ref}_all{dp}_{sites}-filts_{method}.tsv2html.log",
     container:
diff --git a/workflow/rules/6.0_pca.smk b/workflow/rules/6.0_pca.smk
index 58c70da..30b1b6d 100644
--- a/workflow/rules/6.0_pca.smk
+++ b/workflow/rules/6.0_pca.smk
@@ -8,15 +8,15 @@ rule remove_excl_pca_admix:
     results), while allowing them in all other analyses.
     """
     input:
-        "results/datasets/{dataset}/beagles/pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+        "results/datasets/{dataset}/beagles/pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
     output:
-        "results/datasets/{dataset}/beagles/pruned/{dataset}.{ref}_{population}_excl_pca-admix{dp}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+        "results/datasets/{dataset}/beagles/pruned/{dataset}.{ref}_{population}_excl_pca-admix{dp}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
     wildcard_constraints:
         population="all",
     log:
-        "logs/{dataset}/ngsLD/excl_pca_admix_beagle/{dataset}.{ref}_{population}_excl_pca-admix{dp}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
+        "logs/{dataset}/ngsLD/excl_pca_admix_beagle/{dataset}.{ref}_{population}_excl_pca-admix{dp}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/excl_pca_admix_beagle/{dataset}.{ref}_{population}_excl_pca-admix{dp}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
+        "benchmarks/{dataset}/ngsLD/excl_pca_admix_beagle/{dataset}.{ref}_{population}_excl_pca-admix{dp}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
     container:
         shell_container
     params:
@@ -32,11 +32,10 @@ rule pca_pcangsd:
     Produces covariance matrix from SNP genotype likelihood data with PCAngsd.
     """
     input:
-        beagle=lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/pruned/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+        beagle=expand(
+            "results/datasets/{{dataset}}/beagles/pruned/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
             maxkb=config["params"]["ngsld"]["max_kb_dist_pruning_dataset"],
             r2=config["params"]["ngsld"]["pruning_min-weight_dataset"],
-            maj=get_maj,
         ),
     output:
         cov="results/datasets/{dataset}/analyses/pcangsd/{dataset}.{ref}_{population}{dp}_{sites}-filts.cov",
diff --git a/workflow/rules/6.1_admixture.smk b/workflow/rules/6.1_admixture.smk
index 3c00eca..358a86a 100644
--- a/workflow/rules/6.1_admixture.smk
+++ b/workflow/rules/6.1_admixture.smk
@@ -10,10 +10,9 @@ rule ngsAdmix:
     """
     input:
         beagle=expand(
-            "results/datasets/{{dataset}}/beagles/pruned/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+            "results/datasets/{{dataset}}/beagles/pruned/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
             maxkb=config["params"]["ngsld"]["max_kb_dist_pruning_dataset"],
             r2=config["params"]["ngsld"]["pruning_min-weight_dataset"],
-            maj=get_maj,
         ),
     output:
         qopt="results/datasets/{dataset}/analyses/ngsadmix/{dataset}.{ref}_{population}{dp}_{sites}-filts_K{kvalue}.qopt",
@@ -74,10 +73,9 @@ rule evalAdmix:
     """
     input:
         beagle=expand(
-            "results/datasets/{{dataset}}/beagles/pruned/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+            "results/datasets/{{dataset}}/beagles/pruned/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
             maxkb=config["params"]["ngsld"]["max_kb_dist_pruning_dataset"],
             r2=config["params"]["ngsld"]["pruning_min-weight_dataset"],
-            maj=get_maj,
         ),
         qopt="results/datasets/{dataset}/analyses/ngsadmix/{dataset}.{ref}_{population}{dp}_{sites}-filts_K{kvalue}.qopt",
         fopt="results/datasets/{dataset}/analyses/ngsadmix/{dataset}.{ref}_{population}{dp}_{sites}-filts_K{kvalue}.fopt.gz",
diff --git a/workflow/rules/8.0_inbreeding.smk b/workflow/rules/8.0_inbreeding.smk
index c8f0405..9c44f34 100644
--- a/workflow/rules/8.0_inbreeding.smk
+++ b/workflow/rules/8.0_inbreeding.smk
@@ -7,15 +7,14 @@ rule ngsf_hmm:
     Estimate IBD tracts within individual genomes.
     """
     input:
-        beagle=lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/{folder}{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj{pruning}.beagle.gz",
+        beagle=expand(
+            "results/datasets/{{dataset}}/beagles/{folder}{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts{pruning}.beagle.gz",
             folder="pruned/" if config["params"]["ngsf-hmm"]["prune"] else "",
             pruning=(
                 f".pruned_maxkbdist-{config['params']['ngsf-hmm']['max_kb_dist_pruning_pop']}_minr2-{config['params']['ngsf-hmm']['pruning_min-weight_pop']}"
                 if config["params"]["ngsf-hmm"]["prune"]
                 else ""
             ),
-            maj=get_maj,
         ),
     output:
         ibd="results/datasets/{dataset}/analyses/ngsF-HMM/{dataset}.{ref}_{population}{dp}_{sites}-filts.ibd",
diff --git a/workflow/rules/9.0_IBS.smk b/workflow/rules/9.0_IBS.smk
index 4e093e8..0d64818 100644
--- a/workflow/rules/9.0_IBS.smk
+++ b/workflow/rules/9.0_IBS.smk
@@ -9,14 +9,8 @@ rule angsd_doIBS:
         bamlist="results/datasets/{dataset}/bamlists/{dataset}.{ref}_{population}{dp}.bamlist",
         bams=get_bamlist_bams,
         bais=get_bamlist_bais,
-        sites=lambda w: expand(
-            "results/datasets/{{dataset}}/filters/snps/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj_snps.sites",
-            maj=get_maj,
-        ),
-        idx=lambda w: expand(
-            "results/datasets/{{dataset}}/filters/snps/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj_snps.sites.idx",
-            maj=get_maj,
-        ),
+        sites="results/datasets/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts_snps.sites",
+        idx="results/datasets/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts_snps.sites.idx",
     output:
         ibs="results/datasets/{dataset}/analyses/IBS/{dataset}.{ref}_{population}{dp}_{sites}-filts.ibs.gz",
         ibsmat="results/datasets/{dataset}/analyses/IBS/{dataset}.{ref}_{population}{dp}_{sites}-filts.ibsMat",
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 7df114c..95c837e 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -709,90 +709,17 @@ def get_minind(wildcards):
 
 # Determine if docounts is needed for beagle/maf calculation to keep it from
 # slowing things down when it is not. It is only needed if the major and minor
-# alleles are being inferred from counts (-doMajorMinor 2). This would also be
-# needed if using -doMaf 8, but that is not supported currently by the pipeline.
-def get_docounts(wildcards):
-    if str(config["params"]["angsd"]["domajorminor"]) == "2":
+# alleles are being inferred from counts (-doMajorMinor 2) or the minor allele
+# frequency is being inferred by counts (-doMaf 8, >8 possible if count
+# inference is combined with other inferences)
+def get_docounts(wildcard):
+    if (int(config["params"]["angsd"]["domajorminor"]) == 2) or (
+        int(config["params"]["angsd"]["domaf"]) >= 8
+    ):
         return "-doCounts 1"
     return ""
 
 
-# Determine how what -doMajorMinor value to pass to Beagle/MAF calculation. The
-# primary way minor and major will be inferred is set in the config, however,
-# sometimes the pipeline may set these from a -sites file, for instance when
-# polarizing major/minor in pops to the dataset major/minor.
-def get_majmin(wildcards):
-    maj = wildcards.maj
-    pop = wildcards.population
-    polarize = config["params"]["angsd"]["popmafmaj"]
-    configmaj = config["params"]["angsd"]["domajorminor"]
-    # If desired major is reference, always use -doMajorMinor 4
-    if maj == "ref":
-        return "-doMajorMinor 4"
-    # If desired major is ancestral, always use -doMajorMinor 5
-    if maj == "anc":
-        return "-doMajorMinor 5"
-    # If desired major is major of all samples, use -doMajorMinor 3 for pops
-    if (pop != "all") & (polarize == "all"):
-        return "-doMajorMinor 3"
-    # In all other cases, use the configured value
-    return f"-doMajorMinor {configmaj}"
-
-
-# Determine which sites file to use for Beagle/MAF calculation. In almost all
-# cases, this is the filtered sites lists. In the event the user wants
-# population Beagle/MAFs to be polarized to the major across all samples, the
-# sites list produced by the all samples Beagle will be used.
-def get_sitesfile(wildcards):
-    wildmaj = wildcards.maj
-    pop = wildcards.population
-    polarize = config["params"]["angsd"]["popmafmaj"]
-    configmaj = str(config["params"]["angsd"]["domajorminor"])
-    if (pop != "all") & (polarize == "all") & (configmaj in ["1", "2"]):
-        return {
-            "sites": "results/datasets/{dataset}/filters/snps/{dataset}.{ref}_all{dp}_{sites}-filts.{maj}maj_snps.sites",
-            "idx": "results/datasets/{dataset}/filters/snps/{dataset}.{ref}_all{dp}_{sites}-filts.{maj}maj_snps.sites.idx",
-        }
-    return filt_depth(wildcards)
-
-
-# In the event we do polarize to the major allele across all samples within the
-# population Beagle/MAF files, it may mean that fixed sites within the
-# populations are interesting. We'll override the user's set -minMaf and
-# -SNP_pval options in that case to keep any site that was variable in the
-# dataset, even if not in one population.
-def get_snppval_maf(wildcards):
-    pop = wildcards.population
-    snppval = config["params"]["angsd"]["snp_pval"]
-    minmaf = config["params"]["angsd"]["min_maf"]
-    polarize = config["params"]["angsd"]["popmafmaj"]
-    configmaj = str(config["params"]["angsd"]["domajorminor"])
-    if (pop != "all") & (polarize == "all") & (configmaj in ["1", "2"]):
-        return "-SNP_pval 1 -minMaf -1"
-    return f"-SNP_pval {snppval} -minMaf {minmaf}"
-
-
-# Determine which major to set in the filename
-def get_maj(wildcards):
-    pop = wildcards.population
-    configmaj = str(config["params"]["angsd"]["domajorminor"])
-    polarize = config["params"]["angsd"]["popmafmaj"]
-    if configmaj not in ["1", "2", "4", "5"]:
-        raise ValueError(
-            f"Config invalid - you have set a 'domajorminor' parameter "
-            f"incompatible with this workflow. You can only select from 1, 2, "
-            f"4, and 5 for -doMajorMinor at this time. Please change the "
-            f"'domajorminor' entry in the config file to one of these values."
-        )
-    if configmaj == "4":
-        return "ref"
-    if configmaj == "5":
-        return "anc"
-    if (pop in pop_list) & (polarize == "population"):
-        return "pop"
-    return "all"
-
-
 # Determine whether transitions should be removed based on user configuration
 def get_trans(wildcards):
     if config["params"]["angsd"]["rmtrans"]:
@@ -842,6 +769,21 @@ def get_excl_ind_cols(wildcards):
 # Kinship
 
 
+## Get beagle file for input to ngsrelate (either pruned or not)
+def get_ngsrelate_input(wildcards):
+    if config["params"]["ngsrelate"]["prune"]:
+        return {
+            "beagle": expand(
+                "results/datasets/{{dataset}}/beagles/pruned/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+                maxkb=config["params"]["ngsld"]["max_kb_dist_pruning_dataset"],
+                r2=config["params"]["ngsld"]["pruning_min-weight_dataset"],
+            ),
+        }
+    return {
+        "beagle": "results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.beagle.gz"
+    }
+
+
 ## Get all possible kinship estimate pairings
 def get_kinship(wildcards):
     sam = get_samples_from_pop("all")