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Loss of heterozygosity analysis from SNV files

Hi All, Is there any way to identify the Loss of heterozygosity region from the blood and tumor snv vcf files? Or any cut-off for minimum number of homozygous SNPs in a segment to be called a LOH? Thanks

next-gen sequencing
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updated by Bogdan Bogdan • written by rse rse

3 answers

I think Varscan2 outputs LOH events from tumot-normal pair.

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written by poisonAlien poisonAlien

True. Use the processSomatic subcommand for matched-normal samples.

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written by ATpoint ATpoint

Thank you Yes, VarScan2 outputs LOH events from tumor-normal pair, but these are SNVs only. And since LOH is a region of allelic imbalance. How to get the region of LOH from these SNP-Indels?

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written by rse rse

I think that the regions of LOH are labelled as ""SS=3" in the vcf file from VARSCAN.

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written by Bogdan Bogdan

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