1. Community
2. Special GATK Use Cases
3. How do I call variants from somatic RNA data?

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
• April 23, 2021 21:03
• 0 votes

1. Community
2. Special GATK Use Cases
3. How do I call variants from somatic RNA data?

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
• April 23, 2021 20:32
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1. Community
2. General Discussion
3. RNAseq short variant discovery (SNPs + Indels)

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
• April 21, 2021 23:54
• 0 votes

1. Community
2. Germline
3. Data pre-processing for variant discovery - BaseRecalibrator, vcf input?

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...

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• Peiwen Li
• April 21, 2021 19:27
• Edited
• 0 votes