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.
cnvkit.py 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/cnvkit.py", line 11, in <module> args.func(args) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 308, in _cmd_target args.split, args.avg_size) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 327, in do_targets ['chromosome', 'start', 'end', 'name']) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/gary.py", 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/frame.py", line 939, in from_records first_row = next(data) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/target.py", line 287, in split_targets for chrom, start, end, name in region_rows: File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/target.py", line 209, in shorten_labels for row in interval_rows: File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/target.py", line 21, in assign_names ref_genes = read_refflat_genes(refflat_fname) File "/Z/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/target.py", 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/target.py", 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 ??
Sorry for the late reply, you were right. I needed to update the version of CNVkit. Thanks !!!