I have some WES data - GRCh37

[Pharmacogenetecist]

I have some WES data - GRCh37 I would like to run HISAT HLA typing on. How do I specify Hg19 and not grch38 to be used? Thanks.

[marchoeppner]

Not a developer of this tool - but:

Hisat genotype requires unmapped reads as input and returns HLA calls. So it is of no consequence what reference you prefer (but you really should move on from GRCh37/hg19, it's been superseded byGRCh38 for a full decade now and contains many well documented errors). If you only have a BAM file at hand, you can extract the reads as paired-end fastq again using e.g. samtools fastq : http://www.htslib.org/doc/samtools-fasta.html

Hope this helps /M