Question: How to run ABSOLUTE with WGS bam files ?
1
gravatar for subhajit06
3.5 years ago by
subhajit06110
United States
subhajit06110 wrote:

Dear all,

I have a question regarding Copy Number analysis using ABSOLUTE software from Broad Institute.

I want to call CNA for a Tumor with matched Normal and I have both Tumor and Normal bam files.

I have installed ABSOLUTE but I am not sure how to use it for NGS data. I think the example that is given in their website is for array data not for NGS.

thanks much,

--Subhajit

ADD COMMENTlink modified 3.5 years ago by purplerainf0 • written 3.5 years ago by subhajit06110
0
gravatar for purplerainf
3.5 years ago by
purplerainf0 wrote:

Hi Subhajit,

I'm not an expert and also trying to run ABSOLUTE with WES data but I think I can help you.

You can use VarScan & DNAcopy (of BioConductor) to convert your bam files to segment data for the ABSOLUTE.
This link will be helpful for you.
http://varscan.sourceforge.net/copy-number-calling.html

By following the recommended workflow 1~3 in the linked page, you can get a segment file you need.

Please note that when you run ABSOLUTE, you should specify copy_num_type="total" for this type of input data.

Best wishes,
Yunku.

ADD COMMENTlink written 3.5 years ago by purplerainf0

You should not try to use varscan to call CN on WGS. Instead, you should use something like copyCat, or others that support WGS http://omictools.com/somatic-cna-detection-category

ADD REPLYlink written 3.5 years ago by Chris Miller21k

Hi Chris, Thanks for your reply. Does copyCat handle WXS data ??

ADD REPLYlink written 3.4 years ago by subhajit06110

No. VarScan, linked above, is a fine choice for calling copy number from exomes.

ADD REPLYlink written 3.4 years ago by Chris Miller21k

Thanks Yunku for your help and Sorry for my late reply.

ADD REPLYlink written 3.4 years ago by subhajit06110
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