This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Copy Number Variation Tools For Illumina Hiseq Paired End Data (Whole Genome)?

I have illumina HiSeq paired end data (whole genome). I am looking for copy number variation tools to try. Thus far i have found cnv-seq(http://tiger.dbs.nus.edu.sg/cnv-seq/) or svdetect (cnv ---http://svdetect.sourceforge.net/Site/Manual.html).

I am constantly running out of memory when i use svdetect with window size 160 and step 40. i can increase the window and step but then i don't get the cnv at all.

for cnv-seq..i donot get any meaningful output.

Any help is really appreciated.

Thanks Meraj

cnv illumina hiseq paired
• 6,514 views • link
updated by irsan007 • irsan007 • written by Hmm • Hmm

Are your data from a tumor, tumor/normal pair, or just germline sample?

• 5 views • link
written by Sean Davis Sean Davis

i have one large merged bam for tumor and and one for normal.

• 0 views • link
written by Hmm • Hmm

3 answers

[?] There are a number of tools for doing this, depending on what you want to detect. For tumor/normal pairs, I wrote a small package, ngCGH, that simply uses coverage to estimate relative copy number in the tumor versus the normal. A small script is included to segment the resulting output if that is a goal. The code is very simple, should use very little memory and will generally give a very good overview of your data. While usable, I wouldn't consider it "production" yet, but feel free to give it a try. If there are other formats to which you would like to convert, let me know.
[?]

In addition to the two you have tried, you might want to consider pindel and/or breakdancer for a more refined view of potential breakpoints.

• 1 views • link
written by Sean Davis Sean Davis

i visited your site and i am definitely going to give this tool a try. I will let you know the results soon. Thanks

• 0 views • link
written by Hmm • Hmm

I am getting the following error mentioned below.

• 0 views • link
written by Hmm • Hmm

Hi there Meraj,

You might be interested in the CNV-tools that are listed on the SEQwiki:

Cheers,

Irsan

• 28 views • link
written by irsan007 • irsan007

Hi Sean I ran the code once it was installed by our sys admin on the cluster and am getting the following error: (any comments)

Traceback (most recent call last):
  File "/packages/python-2.7/bin/ngCGH", line 5, in <module>
    pkg_resources.run_script('ngCGH==0.1.4dev', 'ngCGH')
  File "/packages/python-2.7/lib/python2.7/site-packages/distribute-0.6.19-py2.7.egg/pkg_resources.py", line 499, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/packages/python-2.7/lib/python2.7/site-packages/distribute-0.6.19-py2.7.egg/pkg_resources.py", line 1235, in run_script
    execfile(script_filename, namespace, namespace)
  File "/packages/python-2.7/lib/python2.7/site-packages/ngCGH-0.1.4dev-py2.7.egg/EGG-INFO/scripts/ngCGH", line 80, in <module>
    main()
  File "/packages/python-2.7/lib/python2.7/site-packages/ngCGH-0.1.4dev-py2.7.egg/EGG-INFO/scripts/ngCGH", line 77, in main
    doNormalComparisonCGH(opts)
  File "/packages/python-2.7/lib/python2.7/site-packages/ngCGH-0.1.4dev-py2.7.egg/EGG-INFO/scripts/ngCGH", line 28, in doNormalComparisonCGH
    tread=tfileiterator.next()
  File "csamtools.pyx", line 1285, in csamtools.IteratorRowRegion.__next__ (pysam/csamtools.c:13460)
StopIteration
• 1 views • link
written by Hmm • Hmm

Log in to answer this question.

More posts like this