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

Question

[bioinforesearchquestions]

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)?

Answer 1

[anp375]

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.

[bioinforesearchquestions]

Thanks, anp375 for your answer.