User: jackyen

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jackyen0
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Posts by jackyen

<prev • 8 results • page 1 of 1 • next >
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GATK FilterMutectCalls parameter max germline posterior ?
... Hello, I'm working on a pipeline and running mutect2. I came across the FilterMutectCalls which can add some annotation on the variants. I'm particularly interested in filtering out the germline variants. There's a "--max-germline-posterior" parameter which default is set at 10% of "posterior prob ...
gatk threshold tool mutect2 written 9 months ago by jackyen0 • updated 9 months ago by ATpoint35k
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Comment: C: step wise pipeline for SNP analysis (illumina Ampliseq sequencing)
... Thanks! Is there's a best practice for Illumina's Ampliseq assay? It seems it's very similar to exome except for the mark duplicate step. ...
written 10 months ago by jackyen0
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Comment: A: step wise pipeline for SNP analysis (illumina Ampliseq sequencing)
... Hello, I came across this and is trying to build a pipeline for illumina's ampliseq kit, too. I saw from another post that "soft clipping" should be done before the variant calling step. I'm wondering if someone could explain a bit more. I've heard BBMap could deal with this a bit better than BWA. T ...
written 10 months ago by jackyen0
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Comment: C: filtering the somatic variants
... hi ATpoint, we only have tumor sample. My understanding is that the standard GATK workflow works a little better with a matched normal but in real world it's difficult to design an experiment because the challenges getting both. What would you suggest how to approach this? thanks ...
written 19 months ago by jackyen0
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Comment: A: filtering the somatic variants
... Hello I am wondering if there's any updates on how to filter the somatic variants? do you have any more insight? thanks ...
written 19 months ago by jackyen0
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amplicon_interval vs target interval in Picard's CollectTargetedPcrMetrics
... Hi, I'm trying to run Picard's CollectTargetedPcrMetrics to get some metrics for my truseq amplicon assay. I'm unclear the difference between "AMPLICON_INTERVALS" vs "TARGET_INTERVALS". I think my question is I need a clear understanding of "baits" vs "targets". I google but didn't find a lot but ...
picard ngs next-gen snp sequencing written 2.3 years ago by jackyen0
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Answer: A: What are most recommended / state-of-the-art whole genome FASTQ datasets for ben
... Hi, I'm curious if anyone knows if there's any publically available NA12878 RNA-seq data? Thanks ...
written 2.5 years ago by jackyen0
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uniformity of coverage (pct > 0.2*mean) calculation/tool
... Hi, I'm trying to find tools to calculate uniformity coverage. I tried use bedtools to get the depth metrics but it takes a really long time. I'm wondering if there's other tools that can do similar work? Thanks, Jack ...
exome sequencing written 2.7 years ago by jackyen0 • updated 2.7 years ago by trausch1.5k

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Popular Question 21 months ago, created a question with more than 1,000 views. For uniformity of coverage (pct > 0.2*mean) calculation/tool

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