Question

How to run ABSOLUTE with WGS bam files ?

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8.5 years ago

subhajit06 ▴ 110

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

CNA next-gen ABSOLUTE bam • 4.5k views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 8.5 years ago by subhajit06 ▴ 110

score 0 · Answer 1 · 2016-05-27

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8.5 years ago

purplerainf • 0

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 COMMENT • link 8.5 years ago by purplerainf • 0

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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 REPLY • link 8.5 years ago by Chris Miller 22k

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

ADD REPLY • link 8.4 years ago by subhajit06 ▴ 110

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

ADD REPLY • link 8.4 years ago by Chris Miller 22k

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

ADD REPLY • link 8.4 years ago by subhajit06 ▴ 110

score 0 · Answer 2 · 2020-03-06

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