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How to get SNV abundance in NGS analysis

After SNV calling, I need to find each SNV's abundance, which means the variant's proportion in all reads that contain the position. How to get the value, and what tools I need to use?

ngs snp gatk
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written by biock • biock

1 answer

After variant calling, you should have a VCF file. VCFs contain a DP field both in their INFO and FORMAT columns, indicating total and ALT depth. There is good documentation about VCFs out there. Spend some quality time reading it.

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written by ATpoint ATpoint

Thank you! But I found that it seems to be 'AP' field in FORMAT column which can get ref and alt reads count in VCF file:

##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

Is this right?

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written by biock • biock

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