- ann arbor
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- ann arbor
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- Weisheng Wu
(Quote) Thanks. What's the threshold size of a panel for VQDR to be applicable?
I know that I need at least 30 exome-seq samples to run VQSR. What about samples from a small panel? There are 3000 target regions in this panel, totaling 1.4Mb. Thanks.
I got an error: ERROR MESSAGE: liftoverb37tohg19/0.111653222310455.unsorted.vcf: Unable to create VCF writer What's wrong?
(Quote) Thanks. Sorry I didn't notice that before. But what filtration I should do with these "mixed" variants, since SNP and INDEL have different filtration? Does it make sense to rewrite this kind of position into two lines (one SNP, and…
(Quote) Thanks for replying. I think I'll anyway remove duplicates. What I really wanted to know is that what is the benefit to let HC do downsampling? It doesn't make sense to me to sequence the DNA ultra-deeply but not use all of them in variant c…
I ran HaplotypeCaller on some exome-seq samples with both dedupped reads (>200x coverage) and non-dedupped reads (>2000x coverage, yes, there is a lot of duplication). I was expecting to see the depth from non-dedupped reads is much higher tha…