Replace missing SNPs of one individual with reference alleles in a VCF file

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4.9 years ago

amitgourav.ghosh12 ▴ 70

Hello,

I have a vcf file of about 565 individuals. I want to replace the missing SNPs of one of them (Ancient sample) with the reference alleles.

I was thinking about trying out the following-

$ bcftools +fixploidy phasedVCF-short02.vcf.gz -- -f 2|bcftools +missing2ref - -- -p > phasedVCF-short03.vcf

But it will probably replace the missing sites in all the individuals.

I am bit confused if there is any function in vcftools or bcftools which would specify to do this operation in only one individual instead of all.

SNP bcftools VCFtools sequencing • 1.5k views

ADD COMMENT • link updated 4.9 years ago by zx8754 11k • written 4.9 years ago by amitgourav.ghosh12 ▴ 70

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Does it make sense to fix it for just one sample?

ADD REPLY • link 4.9 years ago by finswimmer 16k

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Good question, I am not so sure. Let me find out how the PCA comes out.

Meanwhile, I have figured out a possible way to do it. I converted my ld-pruned bed, bim and fam file to vcf file in plink. It only has the genotypes without the quality parameters. Probably it would be much easier to convert the "./." to "0/0" using awk for my target sample.

ADD REPLY • link 4.9 years ago by amitgourav.ghosh12 ▴ 70

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The reason to do so because of that sample being an ancient individual had many missing genotypes, thereby messing up my final pca output.

ADD REPLY • link 4.9 years ago by amitgourav.ghosh12 ▴ 70

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