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3.0 years ago
John
•
0
I'm trying to estimate LOH using purity, ploidy estimates from sequenza.
I use cnvkit call option with its default thresholds,
conda activate **cnvkit0.9.7**
cnvkit.py call $tumour_id.recalibrated.cns -y -v $mutect_tumour_dir/$tumour_id/$tumour_id.passed.vcf.gz --purity $purity --ploidy $ploidy -o $tumour_id.call.cns
The output gives me -ve BAF values which im not sure how to interpret
chromosome start end gene log2 baf cn cn1 cn2 depth probes weight
chr16 66669013 69943499 CMTM4,DYNC1LI2,DYNC1LI2,LOC106699570,LOC106699570,LOC106699570,TERB1 -0.871623 -0.211176 1 1 0 71.7805 2818 2418.18
To confirm are LOH regions where cn1!=cn2 and BAF=0. Also what about estimating copy number netural LOH.
Thank you.