sSNV QC

[graceooh]

Hey @maotian06,

I was wondering if you had any experience in getting or plotting any of the following:

1. number of sSNVs 2) overlaps/differences between callers 3) sSNV numbers per chromosome 4) kataegis 5) VAF distribution between callers. It would be wonderful if you could share your scripts or experience.
   Thanks!

Jieun

[maotian06]

1. Number of sSNVs：You should be able to get this from VCFs.
2. Overlaps: you can used my scripts: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/6.0.0-rc.1/maotian-add-muse-workflow/compare-vcf/bash.sh, it will output an venn plot for each sample and a comparsion result. You might need to adjust the script to suit your data.

3. sSNV numbers per chromosome: You should get from VCF.
4. kataegis: Check the [SeqKat package] (https://github.com/uclahs-cds/public-R-SeqKat)
5. VAF distribution: I think @WuSelina and @sorelfitzgibbon have some scripts?

[graceooh]

Ok I don't know why I wrote 1&3 😂 Thank you!

[sorelfitzgibbon]

Here’s a link to @WuSelina's PR for “creating a stripplot of average adjusted VAFs for sSNVs called by each algorithm” uclahs-cds/project-disease-KidneyTumor-GHLR-000108-SubclonalArchitecture#3