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Remove GATK 4.0.0 DP Fix #125

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Remove GATK 4.0.0 DP Fix #125

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9 changes: 0 additions & 9 deletions pixy/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -295,9 +295,6 @@ def read_and_filter_genotypes(
Filters out non-SNPs, multi-allelic SNPs, and non-variant sites. Optionally masks out
non-target sites based on a provided list (`sites_list_chunk`).

Variants for which the depth of coverage (`DP`) is less than 1 are considered to be missing
and replaced with `-1`.

If the VCF contains no variants over the specified genomic region, sets `callset_is_none` to `True`.

Args:
Expand Down Expand Up @@ -326,7 +323,6 @@ def read_and_filter_genotypes(
"CHROM",
"POS",
"calldata/GT",
"calldata/DP",
"variants/is_snp",
"variants/numalt",
],
Expand All @@ -343,11 +339,6 @@ def read_and_filter_genotypes(
# if the callset is NOT empty (None), continue with pipeline
callset_is_none = False

# fix for cursed GATK 4.0 missing data representation
# forces DP<1 (zero) to be missing data (-1 in scikit-allel)
# BROKEN HERE <- add if statement to check if DP info is present!
callset["calldata/GT"][callset["calldata/DP"] < 1, :] = -1

# convert to a genotype array object
gt_array = allel.GenotypeArray(allel.GenotypeDaskArray(callset["calldata/GT"]))

Expand Down
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