Question: CNVkit segmetrics error
0
gravatar for SPDouglas
2.1 years 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 • 644 views
ADD COMMENTlink modified 2.1 years ago by Eric T.2.6k • written 2.1 years ago by SPDouglas0
0
gravatar for Eric T.
2.1 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k 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 2.1 years ago by Eric T.2.6k
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