Question: CNVkit segmetrics error
0
gravatar for SPDouglas
20 months ago by
SPDouglas0
Finland
SPDouglas0 wrote:

Hi, I'm trying to do CNV analysis on germline samples. However, I'm a newbie in this bioinformatics thing so I'm not sure if I'm doing something wrong because I keep getting this error when I try to do the segmetrics. Here's my batch:

cnvkit.py batch ~/downloads/WM/0158.bam -n -t ~/downloads/WM/Exome-MedExome.bed -f ~/downloads/WM/Homo_sapiens.GRCh37.dna.primary_assembly.fa --access data/access-5k-mappable.grch37.bed --output-reference flat_reference0158.cnn -d test/WM/

cnvkit.py segmetrics 0158.cnr -s 0158.cns --ci --sem

and I get this:

Traceback (most recent call last): File "/Users/xx/anaconda3/bin/cnvkit.py", line 13, in <module> args.func(args) File "/Users/xx/anaconda3/lib/python3.6/site-packages/cnvlib/commands.py", line 1259, in _cmd_segmetrics args.interval_stats, args.alpha, args.bootstrap) File "/Users/xx/anaconda3/lib/python3.6/site-packages/cnvlib/segmetrics.py", line 42, in do_segmetrics for statname in location_stats: TypeError: 'NoneType' object is not iterable

Help?

germline cnv wes • 561 views
ADD COMMENTlink modified 20 months ago by Eric T.2.5k • written 20 months ago by SPDouglas0
0
gravatar for Eric T.
20 months ago by
Eric T.2.5k
San Francisco, CA
Eric T.2.5k wrote:

Sorry for the trouble. This was a bug in the 0.9.2 release. I've released a new version 0.9.3 that includes a fix, so you can upgrade to get a functioning CNVkit installation.

ADD COMMENTlink written 20 months ago by Eric T.2.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 873 users visited in the last hour