APOBEC

Analyzing C->T mutations

A collection of perl and R scripts to format COSMIC mutational datasets and extract mutational signature information.

VCF filtering

SNPs:

• QD < 2.0
• FS > 60.0
• MQ < 40.0
• MQRankSum < -12.5
• ReadPosRankSum < -8.0

Indels:

• QD < 2.0
• FS > 200.0
• ReadPosRankSum < -20.0

note mapping quality filters are not recommended for indels https://qcb.ucla.edu/wp-content/uploads/sites/14/2017/08/gatkDay3.pdf

https://github.com/jakewendt/notebooks/blob/master/20190304-Mutation-Signatures.ipynb

https://github.com/mcjarvis/Mutation-Signatures-Including-APOBEC-in-Cancer-Cell-Lines-JNCI-CS-Supplementary-Scripts

https://academic.oup.com/jncics/article/2/1/pky002/4942295

https://github.com/raerose01/deconstructSigs

https://cancer.sanger.ac.uk/cell_lines

https://docs.google.com/document/d/1l4H4r6vZ8Y0B11p-RGfEbjWStoUl65211_FWE6Mz2kc/edit#

Continuation of Mutation Calling for Tumor-only Data

https://cancer.sanger.ac.uk/cosmic/signatures/SBS/

CCLS/20190205-vcf-tumor-normal