Peiwen Li
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Activity overview
Latest activity by Peiwen Li-
Peiwen Li commented,
Hi Genevieve Brandt (she/her), I have a confusion on the "RNAseq short variant discovery (SNPs + Indels)" GATK Best practices workflow. It suggests to use per-sample variant calling for RNAseq data...
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Peiwen Li commented,
Hi Genevieve Brandt (she/her), Thank you for your replies and I am sorry I posted my questions to the wrong place. I am looking to find differences between my samples and a reference. And after re...
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Peiwen Li created a post,
How do I call variants from somatic RNA data?
AnsweredHi, I have fish liver and brain mRNAseq reads that I would like to call variants from. I am following the "RNAseq short variant discovery (SNPs + Indels)" GATK Best practices workflow which can be ...
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Peiwen Li commented,
Hi Jay Singh, I have the some question. Did you figure out which variant caller to use for somatic RNAseq data, HaplotypeCaller or Mutect2? Thanks, Peiwen
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Peiwen Li commented,
Hi, I have a similar situation as Arye; I am following the GATK best practices workflow for my non-human organism's data, and I am now in Step Base Quality Score Recalibration (BQSR), and yet the s...