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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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genemetrics is reporting genes from first chromosome only #648

Closed npojo closed 3 years ago

npojo commented 3 years ago

Hi, I am running cnvkit.py genemetrics -o results.txt S.cnr; S.cnr includes 24 chromosomes but results.txt reports only chr1 genes. I have tested a mock cnr file:

chromosome start end gene depth log2 weight chr1 10000 11000 A 500 2 0.5 chr1 12000 13000 A 500 2 0.5 chr1 14000 15000 A 500 2 0.5 chr1 16000 17000 A 500 2 0.5 chr1 20000 21000 B 500 2 0.5 chr1 22000 23000 B 500 2 0.5 chr1 24000 25000 B 500 2 0.5 chr1 26000 27000 B 500 2 0.5 chrX 26000 27000 C 500 2 0.5

Which reports genes A and B.

However, the following cnr file reports only gene A:

chromosome start end gene depth log2 weight chr1 10000 11000 A 500 2 0.5 chr1 12000 13000 A 500 2 0.5 chr1 14000 15000 A 500 2 0.5 chr1 16000 17000 A 500 2 0.5 chr2 20000 21000 B 500 2 0.5 chr2 22000 23000 B 500 2 0.5 chr2 24000 25000 B 500 2 0.5 chr2 26000 27000 B 500 2 0.5 chrX 26000 27000 C 500 2 0.5

I have tested several other cnr files leading to the same conclusion. If chr1 is missing, the next chromosome in line is reported (e.g. chr2). Version is 0.9.8. Any ideas? Thanks

tetedange13 commented 3 years ago

Hi @npojo,

It is a known bug of CNVkit (see section "bug fixes" subsection called genemetrics, diagram, scatter) => Has been fixed with CNVkit v0.9.9, so please update to latest release and tell us if this solved your problem?

Hope this helps. Have a nice day. Felix.

npojo commented 3 years ago

Thank you Felix! Just tested with V0.9.9 and now it works fine.

tetedange13 commented 3 years ago

Nice ! So could you please close this issue @npojo ?

Have a nice day. Kind regards. Felix.