Dear all,
i tried to use estimated purity to adjust the allele specific copy number output from cnvkit, but it would generate minus copy number integer value.
below is my command.
cnvkit.py call sample.cns -v sample.vcf --purity 0.39 -m clonal -o sample_purity.call.cns
below is the output .cns file with minus integer copy number value
chromosome start end gene log2 baf cn cn1 cn2 depth probes weight
2 236578628 237490302 AGAP1,GBX2,ASB18,IQCA1,ACKR3 -9.96578 0.00387202 -1 0 -1 26.4653 99 49.9862
did i use cnvkit in wrong way?
thanks.
Hi, there. I also use estimated purity to adjust integer values. but the cn1 I got -3 and cn2 got 0, what it means? Can I see it as LOH region?