We are analyzing the WES 500K files and when I remove variants for DP, allele balance, and low complexity it seems like 15-17% (both SNPs and indels) of variants on a chromosome are being removed. Does that seem like too much?
It sounds pretty normal to me though we didn't use the same filter. In our experiment with WGS that we provide tutorial, we removed much more due to lots of low frequency variant. Let's hear from other members too though.
Curious to hear what's your experience with other sequencing data too.
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It sounds pretty normal to me though we didn't use the same filter. In our experiment with WGS that we provide tutorial, we removed much more due to lots of low frequency variant. Let's hear from other members too though.
Curious to hear what's your experience with other sequencing data too.
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