negative BAF values OH
0
0
Entering edit mode
27 days 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.

LOH cnvkit BAF • 53 views
ADD COMMENT

Login before adding your answer.

Traffic: 2292 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6