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For multisample VCF, should I filter the variants based on allele depth (AD) or Overall depth ?

Hi All,

For the below vcf record, first sample is G/G (1/1-Heterozygous alternate) with allele depth of 101 reads. Whereas for the second sample is also G/G(1/1) with allele depth of 1 read. Overall depth is 102. If I filter vcf records base on DP >10. Then I will get this vcf record. But the second sample has only one 1 supporting read.

1) For multisample VCF, should I filter the variants based on allele depth (AD) or Overall depth (DP)?

2) What is VQSRTrancheBOTH99.00to99.90 (it is present in filter column)?

enter image description here

vcfs snps variants depth dnaseq
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updated by anp375 anp375 • written by bioinforesearchquestions bioinforesearchquestions

1 answer

if you used VQSR, correctly, you shouldn't need to filter anymore. Other than that, read about GATK's variant filtration. Their defaults are usually good.

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written by anp375 anp375

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