Coverage requirements for LOHHLA

[ahwanpandey]

Hello,

What coverage do you recommend to run this tool for Whole Genome Sequencing? Is 30x Normal and 60x Tumor sufficient?

Thanks, Ahwan

[ahwanpandey]

I am getting the following message in the log files for most of my samples when running in Tumor+Normal mode:

No position has greater than minimum coverage filter for hla_a

No position has greater than minimum coverage filter for hla_b

No position has greater than minimum coverage filter for hla_c

I am using the following settings:

--minCoverageFilter=10 \
--kmerSize=50 \
--numMisMatch=1 \
--mappingStep=TRUE \
--fishingStep=TRUE \
--plottingStep=TRUE \
--coverageStep=TRUE 

If I run the samples by themselves, here's a glance at the overages once mapped to the HLA alleles. I've included all HLA-A, HLA-B and HLA-C for Tumor/Normal

HLA-A

Tumor

Normal

HLA-B

Tumor

Normal

HLA-C

Tumor

Normal