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Germline short variant discovery (SNPs + Indels) best practice for WES and gene panel

I wonder what modification is needed for the Germline short variant discovery (SNPs + Indels) best practice when being applied to WES and gene panel.

Here is my own understanding, could someone give any opinion?
WES: no modification is needed
gene panel: in the Filter Variants step, use hard filtering instead of VQSR. Are there any recommendation on how to do the hard filtering, i.e. the parameters and their cutoffs?

For example, I see others using the following:
variant site filtering: min(AB) > 15% for SNP, and > 20% for InDel; AB: Allele Balance
genotype filtering: min(QD)>2 and min(DP) > 6 for SNP, and 4 and 9 for Indel.

Best Answer


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