Get Unique variants (SNPs and Indels) using bcf tools

Question

[mahanish123]

I completed the local alignment and have 19 VCF files. How can I get unique variants - SNPs and Indels from these 19 VCF files so the variants won't repeat in each of 19 samples using bcf tools ?

Answer 1

[Pierre Lindenbaum]

 bcftools merge -0 indexed*.vcf.gz | bcftools view -i '(count(GT="AA")==1 && count(GT="het")==0)  ||(count(GT="AA")==0 && count(GT="het")==1)'

[mahanish123]

What does this GT="AA" and GT="het" means ?

[Pierre Lindenbaum]

https://samtools.github.io/bcftools/bcftools.html#expressions

I fixed the expression above btw

[mahanish123]

Thanks. I will try it.