Merge different VCFs from multiple individuals including singletons

Question

[Mari]

Hi.

I want to have a VCF file with multiple individuals from individually genotyped each sample. However, as I genotyped them separately, loci with 0|0 genotypes (in reality) in an individual are not recorded in the vcf file.

Can I incorporate polymorphic regions with 0|0 genotypes in some individuals? (not 0|0 in all individuals, of course).

When I tried naively it with VCFtools (0.1.16),

vcf-merge  indivi1.SNVs.vcf.gz indivi2.SNVs.vcf.gz indivi3.SNVs.vcf.gz | bgzip -c > merge.SNV.vcf.gz

0|0 locus (in reality) was recorded as ./. (in output.vcf), but I want to convert (or re-genotype, restore) ./. into 0|0 if they are likely to be 0|0, not low-quality locus (not genotyped) in that individual.

The original individual vcf files have quality information (as below). I also have BAM files and ref.fa.

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
ssa01 38352 . C T 696 . . GT:GQ:DP:AF:PS 1|0:696:2:0.5:38352
ssa01 106281 . A G 720 . . GT:GQ:DP:AF:PS 0|1:720:4:0.25:38352
ssa01 106522 . C T 789 . . GT:GQ:DP:AF:PS 0|1:789:4:0.25:38352

Thank you very much.

Answer 1

[Ram]

VCFTools is not actively maintained, I think. Try bcftools merge instead.

[Mari]

It worked! Thank you very much! (I am sorry, I am not sure how to make a post "closed" or "solved")

bcftools merge -l SNVvcf.list --force-samples --missing-to-ref -Oz -o bcfmergeSNV.vcf.gz

[Ram]

I've moved my comment to an answer. Please accept it to mark the post as solved.

[Ram]

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