Loss of heterozygosity analysis from SNV files

Question

[rse]

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

Answer 1

[poisonAlien]

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

[ATpoint]

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

Answer 2

[rse]

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?

Answer 3

[Bogdan]

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