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## Feature request
### Tool(s) or class(es) involved
CreateSomaticPanelOfNormals
### Description
Currently, CreateSomaticPanelOfNormals emits sites-only VCFs. Some downstream tools require…
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Hello,
I'm running into an error with mutect2 (`java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN`) when using a pair of FASTQ files with yeast sequence reads. Ot…
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When doing paired variant calling, how can I have both the paired (somatic) and unpaired variant statistics in multiqc? Right now, when specifying germline as well as somatic callers, I get multiqc 'g…
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Hello.
Iв this possible to run single VEP run with with multiple input CSV files?
I tried to pass 2 `file` args to command:
`
$VEP --fork $PROGRAMNUMCPUS --input_file $inputVCFFile --format vcf --…
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Thank you everyone for your contributions towards this documentation effort.
Instructions from @vdauwera ~~to follow~~ at [this Google doc](https://docs.google.com/a/broadinstitute.org/document/d/1r…
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Hi, I noticed that previous post #1715 have discussed this problem, I just want to know how to set the parameters in yaml file to support high-depth (about 2000x) panels covering tens of genes. First…
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Hello,
I have a question regarding mutation burden that hopefully you can give me some insight for. I have WGS data for two cohorts. They have been sequenced at different depths:
![image](https:…
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Do you have in mind including Star allele pipeline and CPIC guidlines?
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hello, thanks for supplying such a powerful tool. i have several other questions here.
Q1: can this tools applied to germline and somatic amplicon and Hybrid data, if so, how it decide whether to mar…
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Good morning,
I have a question about pymol. I understand the how hotspot3d predict the clusters. But when I read a paper “Pathogenic Germline Variants in 10,389 Adult Cancers”，Figure 7B in …