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@Sheila said: @metheuse Hi, We don't recommend using VQSR on small targeted data, as there is simply not enough data for the tool to build a proper model. You will need to use hard filtering. -Sheila Thanks. What's the …
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?
@Kurt said: That would be -selectType MIXED I believe. 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 t…
@Geraldine_VdAuwera said: Hi metheuse, There is actually no expectation of getting either more or fewer variants in dedupped reads vs. non-dedupped reads, since you don't know ahead of time if the duplicates support reads that are all ref …
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…