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ExtractHLAread.sh fails when the input file is in .cram format. #70
Description
If starting from an aligned bam/cram file, ExtractHLAread.sh fails when the file is in .cram format.
The samtools command to extract the HLA regions needs to have the -T reference.fasta flag inserted due to the .cram file compression.
Activity
wshuai294 commentedon Mar 5, 2026
Thanks for the feedback! We'll revise it as suggested.
pjgreer commentedon Mar 6, 2026
OK, you may want to add a flag to the ExtractHLAread.sh to point to the user downloaded ref.fasta The ref.fasta and fai files are over 3GB and you probably should not be distributing them.
haveing the -T ref.fasta flag there for .bam files doesnt hurt anything for .bam file reads, but it must be there for .cram files.
and Thanks for the quick response.
wshuai294 commentedon May 12, 2026
Hi, I added -T as suggested. Thx so much!