Question: Error due to annotation file while running target module from CNVkit tool
gravatar for arta
2.5 years ago by
arta560 wrote:

Hi all,

I am working on copy number alteration detection from exome sequencing (both tumor and normal samples) and using cnvkit package. I do have problem while i am preparing the BED file of baited regions. I am running following script and getting error. target access-10kb.spretus_129s1.bed --annotate refFlat.txt --split --short-names -o targets.bed

Detected file format: BED Applying annotations as target names Shortening interval labels Splitting large targets Traceback (most recent call last): File "/Z/tools/bcbio/bin/", line 11, in <module> args.func(args) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/", line 308, in _cmd_target args.split, args.avg_size) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/", line 327, in do_targets ['chromosome', 'start', 'end', 'name']) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/", line 66, in from_rows table = pd.DataFrame.from_records(rows, columns=columns) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/", line 939, in from_records first_row = next(data) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/", line 287, in split_targets for chrom, start, end, name in region_rows: File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/", line 209, in shorten_labels for row in interval_rows: File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/", line 21, in assign_names ref_genes = read_refflat_genes(refflat_fname) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/", line 80, in read_refflat_genes name, _rx, chrom, strand, start, end, _ex = parse_refflat_line(line) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/", line 128, in parse_refflat_line start, end = fields[4:6] ValueError: need more than 0 values to unpack

But when i remove --annotate refFlat.txt, i am able to create targets.bed file. Since annotations are crucial for the downstream analyze to me, i want to keep them during analysis. Below you can find the sample of refFlat.txt file (tab deliminated) which is the same as desired input from documentation

  • 129S1_chr1 215998 218733 Xkr4
  • 129S1_chr1 208914 209708 Xkr4
  • 129S1_chr1 1445713 1445784 Rp1

Any help will be appreciated very much ??

sequencing cnv cnvkit exome • 1.0k views
ADD COMMENTlink modified 2.5 years ago by Eric T.2.6k • written 2.5 years ago by arta560
gravatar for Eric T.
2.5 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

It looks like you're using an older version of CNVkit. The current version is 0.9.0, and the previous version 0.8.5 should also work here. Could you try either of those?

ADD COMMENTlink written 2.5 years ago by Eric T.2.6k

Sorry for the late reply, you were right. I needed to update the version of CNVkit. Thanks !!!

ADD REPLYlink written 2.5 years ago by arta560
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