Why is VCFtools excluding invariable sites?
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7 months ago

I have a vcf file with all genomic sites including invariable, which I generated with the option --ALL-SITES in gatk GenotypeGVCFs. I want to filter that file for quality, coverage etc, but the VCFtools command below excludes all invariant sites. Why? It doesn't seem like it should. I wanna keep them (if they pass filters).

module load vcftools/0.1.14/INTEL-18.0.0

vcftools --gzvcf raw_unfiltered_ALLSITES.vcf --max-missing 0.5 --minQ 30 --minDP 5 --recode --recode-INFO-all --out temp
vcftools • 469 views
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Maybe describe more why you want to keep invariant sites in a variant call file? I think VCFs and vcftools are designed with the assumption that these files describe variants.

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Consider using bcftools instead. VCFtools has not been updated for a long time and it won't be updated (according to its author). bcftools acts more reasonably than VCFtools.

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