xHLA is compatible with BAM file against hg38 (no ALT contigs). Supported aligners include:

• BWA-mem with default parameter
• Illumina Isis/Isaac software

For example, reference sequences in the GATK resource bundle contain HLA contigs that might trap reads in those contigs, instead of in region chr6:29844528-33100696 assumed by xHLA.

For BAMs generated with ALT+HLA contigs or with funny alignment parameters, we need to extract all ALT+HLA+unmapped contigs and re-align with BWA-mem using default parameters. Please see bin/get-reads-alt-unmap.sh. An example command for the BAM preparation script is:

bin/get-reads-alt-unmap.sh input.bam output.bam

Then you can run xHLA on the new BAM file after this conversion.

We would like to thank Andrew J. Rech (@andrewrech) for providing an improved version of this script.