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My initiative for doing this truncation is that though HLA-LA is working fine with the full BAM file before chr6 truncation, the processing time was long.
I mapped my data to hg38 (reference is whole genome) and truncated a sub-dataset of only chr6 entries with following comment:
When feeding the only-chr6 BAM file into the HLA-LA, I got the following error code after the 'Extract unmapped reads... ' checkpoint:
Issue seems to be similar to #88, but still different.
Any help would be appreciated.
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