Extract reference and alternate SNPs for different samples

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7 months ago

gubrins ▴ 290

Hi all,

I have a vcf file and I would like to extract all SNPs that are alternate for some specific samples but reference for the other samples. Should be quite easy but I did not manage. Any recommendation about any software that could help me? I imagine this could be implemented with vcftools?

Thanks in advance!

vcftools bcftools SNPs • 458 views

ADD COMMENT • link updated 7 months ago by GenoMax 141k • written 7 months ago by gubrins ▴ 290

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bcftools should have an option for this. What have you tried?

ADD REPLY • link 7 months ago by Ram 43k

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see Find groups of SNP in a multi sample VCF with bcftools ;
Unphase a VCF file ;
Find groups of SNP in a multi sample VCF with bcftools ;
multisample vcf filter with bcftools, condition true for ALL samples ;
How to remove shared SNP from a VCF with multiple individuals ; etc...

ADD REPLY • link updated 7 months ago by GenoMax 141k • written 7 months ago by Pierre Lindenbaum 161k

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