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CNVkit LOH on old version

Hello all,

I use CNVkit for my workflow with the WES bam files. I am curious that this kit had a function to calculate loss of heterozygosity (loh) via a vcf file on an old version of this. I am actually interested in analyzing for LOH, so is there an alternative? I see a tumor heterogeneity section I could follow on CNVkit, but not sure what to do. Any advice is appreciated; maybe I can write my own LOH calculation via my VCFs?

Thanks, Roy

of cnvkit loh loss heterozygosity cnv
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written by Roy • Roy

I regularly use FACETS for this purpose. You can find the paper here if you are interested.

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written by iraun iraun

Thanks, this looks intriguing. I only have the tumor BAM file, is the normal required?

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written by Roy • Roy

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