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
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subhajit06
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.
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
Hi Chris, Thanks for your reply. Does copyCat handle WXS data ??
No. VarScan, linked above, is a fine choice for calling copy number from exomes.
Thanks Yunku for your help and Sorry for my late reply.
Hello,
Can anyone here explain the input format ABSOLUTE use for DNA sequencing data? Specifically, ABSOLUTE requires the input data to have at least four columns: "Chromosome", "Start", "End", "Num_Probes" and "Segment_Mean".
For my sequencing data, I have done the segmentation already, and I have "Chromosome", "Start", "End", plus the number of reads mapped to the segment in tumor sample "d_T", and the number of reads mapped to the segment in matched normal sample "d_N". So, I'm wondering what do "Num_Probes" and "Segment_Mean" mean for ABSOLUTE and how can I convert my data into them?
Thanks so much!
Best, Siyuan
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