problem running MuSiC from WashU

[Lien]

Dear all,

I have exome data sets of cancer samples, and would like to find out which pathways are significantly mutated. Therefore, I thought using the MuSiC tools from WashU. Apparently, there aren't a lot of people who use it, since I didn't find a lot of threads about it. But if anyone could help me, this would be much appreciated.
For the Path-Scan analysis, I first have to run bmr calc-covg. But when I use the following command, I receive an error.

genome music bmr calc-covg --bam-list=/music/bam_list --output-dir=/music/ --reference-sequence=/human_g1k_v37.fasta --roi-file=/music/all_coding_exons.tsv

Usage: calcRoiCovg <bam1> <bam2> <roi_file> <ref_seq_fasta> <output_file> [min_depth_bam1 min_depth_bam2 min_mapq]
Defaults: min_depth_bam1 = 6, min_depth_bam2 = 8, min_mapq = 20
NOTE: ROI file *must* be sorted by chromosome/contig names

Failed to execute: calcRoiCovg /music/normal.bam /music/tumor.bam /music/all_coding_exons.tsv /human_g1k_v37.fasta /music/roi_covgs/TCGA-88824362.covg 6 8 20
Failed to execute: 'gmt music bmr calc-covg-helper --normal-tumor-bam-pair "TCGA-88824362 /music/normal.bam /music/tumor.bam" --roi-file "/music/all_coding_exons.tsv" --reference-sequence "/human_g1k_v37.fasta" --output-file "/music/roi_covgs/TCGA-88824362.covg"'


I don't really know what's causing the error, so I'm not sure where to start looking for problems. Do any of you know what could be happening? I already ensured that all files (bam-files, MAF-file, reference, regions of interest) have the same chromosome naming conventions.

Thanks a lot
Lien

[satish_25]

How to creat ROI and MAF file for MusiC analysis?????

Dear all,

I also want to use MuSiC package for my exome sequencing data and as per its requirements I have to prepare ROI and MAF file. I dont know exactly how to prepare ROI file, I have the bed file but its with probeID not with gene names.. so i dont know how to replace that probeID with gene names??? I cant do this manually because there are around 5000000 probes... so can anyone help me in preparing this ROI file by suggesting some way??? i want to have a look at some ROI files generated by others.... please people help me out.

Thanks,
Satish

[cyriac]

Most of the support for MuSiC is at BioStars.org. Just look for the tag "MuSiC" - http://biostars.org/show/tag/MuSiC+music/. Sample input files are listed in this post - http://biostars.org/p/62793/