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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Allow using reference fasta with reference cnn in cnvkit batch when processing crams #869

Open IvantheDugtrio opened 7 months ago

IvantheDugtrio commented 7 months ago

I get the following error message when trying to process crams. My cram files have @SQ tags that point to a reference path that does not exist on my computer, but I have the reference file. Recreating the path to the references is not practical as each cram has different reference paths. I am looking into samtools reheader but ideally I don't modify these crams in any way.

CNVkit 0.9.10 If -r/--reference is given, options to construct a new reference (-f/--fasta) should not be used. (See: cnvkit.py batch -h)

etal commented 5 months ago

This error is about CNVkit's reference.cnn file, not the FASTA reference genome sequences. If you used -r with an existing file, then you don't need to (and shouldn't) also use -f.