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cgat-developers / cgat-flow

cgat-flow repository
MIT License
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Updated samtools doesn't work with hisat2 in mapping pipeline #124

Open microbialman opened 4 years ago

microbialman commented 4 years ago

Having just done a new CGAT install I ended up with the latest version of samtools (1.10) it has a new way of handling BAM headers that throws an error when I used hisat2 in the mapping pipline (in the step using samtools view to pipe to bam2bam).

I tested using samtools version 1.9 locally and this seems to work still so I guess samtools version might need to be limited? Not sure why the BAM output from hisat2 causes problems.

Acribbs commented 4 years ago

Thanks for the comment, I can take a look at this over the xmas break