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researchapps / polysolver

Singularity port of HLA typing based on an input exome BAM file and is currently infers infers alleles for the three major MHC class I (HLA-A, -B, -C)
MIT License
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Getting 'winners.hla.nofreq.txt' #3

Open terra1666 opened 7 years ago

terra1666 commented 7 years ago

Hello

I'm trying to use polysolver to do HLA typing from exome data. What does it means if I get 'winners.hla.nofreq.txt' instead of 'winners.hla.txt'? I always get this filename as final output and it always shows the specific HLA type as below.

-e HLA-A        -e hla_a_01_01_01_01    -e hla_a_01_01_01_01
HLA-B   -e hla_b_07_02_01       -e hla_b_07_02_01
HLA-C   -e hla_c_01_02_01       -e hla_c_01_02_01

Those are not what I expect to get.

This occurs even when I set inappropriate path for bam file (it complains at first unable to find the bam file, but keeps calculating and gives 'winners.hla.nofreq.txt' finally). I also tried both 0 and 1 flag for 'includeFreq' option, but it doesn't make any change.

Another HLA typing program predicted HLA-A and C, so my exome data should contain enough reads to cover at least HLA-A and C allele.

vsoch commented 7 years ago

hey @terra1666 ! I apologize I can't help with the specifics of the tool, but I'd recommend you reach out to this group http://archive.broadinstitute.org/cancer/cga/polysolver