Genome Music Bmr Calc-Bmr Returning All Zeros Under "Mutations" And "Bmr" In Gene_Mrs File

Question

[sndorman]

Hello,

I am currently running Genome MuSiC to identify significantly mutated genes in my data set. I ran bmr calc-bmr, and only the gene_mrs file was outputted, but the "mutations" and "BMR" columns are all zero. In addition, there was no "overall_bmr" file outputted.

I am assuming this has something to do with "Skipped 22409 mutation(s) that have unrecognized gene names" (below), but my gene_covgs files for this data all appear to be intact, with numbers and NM_ IDs.

I would appreciate any input into why this isn't working - thanks very much!

The STDERR was:

Skipping invalid ROI bitmask Un_gl000228:99283-100663

Skipping invalid ROI bitmask Un_gl000228:99283-100663

Loading per-sample coverages stored in MuSiC/total_covgs

Loading per-gene coverage files stored under MuSiC/gene_covgs/

Running 'joinx1.6 ref-stats' to read reference FASTA and identify SNVs at AT, CG, CpG sites

Parsing MAF file to classify mutations

Finished Parsing the MAF file to classify mutations

Skipped 40496 mutation(s) that are classified as Silent

Skipped 22409 mutation(s) that have unrecognized gene names

Skipped 254 mutation(s) that belong to unrecognized samples

Answer 1

[Chris Miller]

My guess from the output you post is that the data in your MAF file doesn't match one or both of the following:

1) The gene names in your ROI file

2) The sample names in your bam list.

[sndorman]

Thanks! I went through and checked the gene names and hadn't realized that my ROI file had used RefSeq IDs not Entrez/HUGO that are in the MAF file. Calc-bmr ran fine after updating the MAF file.