Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?

Question

[namhaesly]

Hi I'm a new to bioinformatics.

I have a task to analyze WES data using ABSOLUTE R package. I must use ABSOLUTE for that task although there are several tools for the same purpose.

What I found are ABSOLUTE takes an output from HAPSEG or an user-segmented file as input, (http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE/1)

and HAPSEG takes a SNP file as input only from the result of SNP_250K_STY or SNP_6.0 microarray (Affymetrix). (http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/HAPSEG/)

But what I want to analyze are WES data from llumina Hiseq2000.

Is there method to convert these WES data to SNP file for HAPSEG input or user-segemented file for ABSOLUTE input?

[mkaushal]

I think you will find this useful: A: Anyone Has A Working Example On How To Run Broad'S Absolute On Exome Sequencing

Answer 1

[sophiespo]

Hey namhaesly,

You need to create segmentation files for your data. You can use VarScan2 (the copynumber) function, or any other program that computes copy number information. My tool of choice is ExomeCNV though I don't know how supported it is these days.

Then you can add the mutation information (optional). If you call your mutations in VCF format you can annotate them using snpEff, and then convert to MAF format using a tool called vcf2maf.

As you can see there are a lot of steps between having WES data and the correct input data for ABSOLUTE. I am not going to tell you how to generate all the proper files, you can read the help information for each tool.

Here are some links to get you started:

http://varscan.sourceforge.net/

https://secure.genome.ucla.edu/index.php/ExomeCNV_User_Guide

http://snpeff.sourceforge.net/

https://github.com/mskcc/vcf2maf

Good luck!

Answer 2

[Matt]

segmentation files:

cnvkit.py export seg *.cns -o *.seg

and change the column name to look like this: Sample\tChromosome\tStart\tEnd Num_Probes\tSegment_Mean.

maf files:

vcf2maf.pl --input-vcf *.vcf --output-maf *.maf --tumor-id * --normal-id * --vep-path your_vep --vep-data your_vep_cache --ref-fasta $ref --filter-vcf 0 --species homo_sapiens

and change the column name 'Start_Position' to 'Start_position'.

In addition, the ABSOLUTE module has officially been deprecated on December 06, 2021.