For GRCh38 aligned bam

[WangKang-Leo]

Hi, I have a question. Polysolver can support bam (GRCh38), but hlaloh is still using hg19. Is it compatible if I input GRCh38 aligned bam?

[pyc1216]

Hi!
This may not work because the LOHHLAscript.R script extracts HLA-related regions from a BAM file based on hg19 coordinates using samtools view. If using GRCh38, corresponding coordinates need to be modified.

line597:
samtoolsCMD <- paste("samtools view ", BAMDir, '/', BAMfile, " chr6:29909037-29913661 >> ",regionDir,"/",BAMid,".chr6region.sam",sep="")