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wdecoster / cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
MIT License
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Option to exclude contigs in the reference #25

Open SLAment opened 6 months ago

SLAment commented 6 months ago

Hi! Thanks for a great tool. I was wondering if you could implement an option to remove a contig or a list of contigs when calculating the stats. Sometimes I have bacterial contaminations, or the mitochondrial contig has crazy coverage compared to the chromosomes, so I fear those values might inflate upwards the average depth of coverage in the report. Rather than re-map the reads to a reduced reference genome, I think it would be great if Cramino could consider it if asked.

Thanks!

wdecoster commented 6 months ago

Great suggestion. I will add that. Thanks!

wdecoster commented 3 weeks ago

Hi,

While I haven't added this yet, I would just like to point out that you can use samtools to filter the file and pipe that into cramino to read from stdin. That should get you what you want.

Cheers, Wouter