Extract reference and alternate SNPs for different samples

Question

[gubrins]

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!

[Ram]

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

[Pierre Lindenbaum]

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...