What does this GT="AA" and GT="het" means ?
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mahanish123 •
Get Unique variants (SNPs and Indels) using bcf tools
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 ?
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mahanish123 •
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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)'
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Pierre Lindenbaum
https://samtools.github.io/bcftools/bcftools.html#expressions
I fixed the expression above btw
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Pierre Lindenbaum
Thanks. I will try it.
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mahanish123 •
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