Question: Copy Number Variation Tools For Illumina Hiseq Paired End Data (Whole Genome)?
5
gravatar for Hmm
7.4 years ago by
Hmm490
Hmm490 wrote:

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

illumina paired cnv hiseq • 4.0k views
ADD COMMENTlink modified 7.3 years ago by irsan00710 • written 7.4 years ago by Hmm490

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

ADD REPLYlink written 7.4 years ago by Sean Davis25k

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

ADD REPLYlink written 7.4 years ago by Hmm490
3
gravatar for Sean Davis
7.4 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

[?] 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.

ADD COMMENTlink written 7.4 years ago by Sean Davis25k

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

ADD REPLYlink written 7.4 years ago by Hmm490

I am getting the following error mentioned below.

ADD REPLYlink written 7.4 years ago by Hmm490
1
gravatar for irsan007
6.5 years ago by
irsan00710
irsan00710 wrote:

Hi there Meraj,

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

Cheers,

Irsan

ADD COMMENTlink written 6.5 years ago by irsan00710
0
gravatar for Hmm
7.4 years ago by
Hmm490
Hmm490 wrote:

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
ADD COMMENTlink written 7.4 years ago by Hmm490
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: 770 users visited in the last hour