SNPfiltering.md

VCFtools filtering

Remove sex chromosomes so downstream analyses performed on autosomal SNPs

Kakapo Z chromosome: CM013763.1

https://www.ncbi.nlm.nih.gov/nuccore/CM013763.1/

Kakapo W chromosome: CM013773.1

https://www.ncbi.nlm.nih.gov/nuccore/CM013773.1

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Initial VCFtools v1.14 filtering: remove sex chomosomes and filtered for minimum depth of 2 & maximum depth of 30

Input files: variant call format (.vcf)

vcftools --vcf 1_unfilt.vcf --not-chr CM013763.1 --not-chr CM013773.1 --minDP 2 --maxDP 30 --recode

For more details on VCFtools usage, see: https://vcftools.github.io/man_latest.html

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After, --missing-indv to generate file reporting the missingness on a per-individual basis

vcftools --vcf unfilt.vcf --missing-indv

Removed individuals with high missingness >70%

vcftools --vcf filt_sexchr_minmaxdp.vcf --remove-indv <name> --remove-indv <name> --remove-indv <name> --recode

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Filter VCF for inbreeding estimates

Filtered allowing up to 20% missing data

vcftools --vcf maxdp30_mindp2.vcf --max-missing 0.80 --recode

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