Hi MC3 Team --
Is there an official bed file (containing the Exome ROIs) that was used in this mutation analysis?
Many thanks,
James
Created by James White jwhite Hi Dinesh -- Matthew Bailey sent me the following information about the Bed file. There appears to be limited information about the specific ROIs that were used for somatic mutation calling.
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We restricted exome mutation calling to 2 main bed files. These files are (i) a GAF 4.0 exons only .bed and (ii) a target .bed file created by the BROAD.
The GAF and BROAD.bed restriction files were limited to a possible exonic mutation to
94.6Mb GAF bed
82.2Mb BROAD.bed
The GAF and BROAD.bed files may be much larger than you were expecting.
Another piece of information that you may find useful is the annotation/aggregation tool we used to generate our mutations file. This is Dr. Kandoth's vcf2maf tool that harnesses VEP v82 (http://useast.ensembl.org/info/docs/tools/vep/index.html) for annotating variants (https://github.com/mskcc/vcf2maf). At the time we used vcf2maf v1.6.11 and it is currently v1.6.15. This tool is also capable of re-annotating variants based for an alternative version of VEP.
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Hi James,
I'm wondering if you ever got hold of the BED file? If so, can I also get it?
Thanks,
Dinesh