Genome Music - Calc-Bmr

Question

[will.lockwood]

Hi All,

I finally got the calc-covg function in Genome MuSiC to run but now I am having an issue with using the subsequent files to run calc-bmr. I have checked all my input files and everything seems correct. The BAM list, ROI file and reference file are all the same as were used with calc-covg. I have formatted the MAF file according to 2.3 specs. All files use chrN annotations. However, I continue to get the errors such as the following:

Use of uninitialized value within %gene_idx in array element at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 295, <gen20> line 675. Use of uninitialized value within %gene_idx in array element at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 296, <gen20> line 675. Use of uninitialized value within %gene_idx in array element at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 297, <gen20> line 675. Use of uninitialized value within %gene_idx in array element at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 298, <gen20> line 675. Use of uninitialized value within %gene_idx in array element at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 299, <gen20> line 675. Use of uninitialized value within %gene_idx in array element at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 300, <gen20> line 675. Use of uninitialized value within %gene_idx in array element at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 301, <gen20> line 675.

It then goes on to report the following:

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

However, it says that none of the mutations in my MAF are in the ROI, which is not true.

The only issue that I can think of is something about my MAF file. Is there anything extra that calc-bmr requires that is not in the TCGA MAF documentation page? I have formated everything according to their specs and have the #version 2.3 as a headed below the column names row.

Any help would be greatly appreciated.

Thanks,

Will

[naruto1nrt]

I meet that error too:

Use of uninitialized value within %gene_idx in array element at /PUBLIC/software/HEALTH/04lib/perl/lib/perl5/site_perl/5.18.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 295, <GEN25> line 20312.
Use of uninitialized value within %gene_idx in array element at /PUBLIC/software/HEALTH/04lib/perl/lib/perl5/site_perl/5.18.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 296, <GEN25> line 20312.
Use of uninitialized value within %gene_idx in array element at /PUBLIC/software/HEALTH/04lib/perl/lib/perl5/site_perl/5.18.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 297, <GEN25> line 20312.
Use of uninitialized value within %gene_idx in array element at /PUBLIC/software/HEALTH/04lib/perl/lib/perl5/site_perl/5.18.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 298, <GEN25> line 20312.
Use of uninitialized value within %gene_idx in array element at /PUBLIC/software/HEALTH/04lib/perl/lib/perl5/site_perl/5.18.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 299, <GEN25> line 20312.
Use of uninitialized value within %gene_idx in array element at /PUBLIC/software/HEALTH/04lib/perl/lib/perl5/site_perl/5.18.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 300, <GEN25> line 20312.
Use of uninitialized value within %gene_idx in array element at /PUBLIC/software/HEALTH/04lib/perl/lib/perl5/site_perl/5.18.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 301, <GEN25> line 20312.
Running 'joinx1.6 ref-stats' to read reference FASTA and identify SNVs at AT, CG, CpG sites
RUN: joinx1.6 ref-stats --ref-bases --bed /tmp/gm-genome_sys-2014-08-26_05_00_09--j_vA/anonymous0 --fasta /PUBLIC/database/HEALTH/genome/human/b37_gatk/human_g1k_v37_decoy.fasta --output /tmp/gm-genome_sys-2014-08-26_05_00_09--j_vA/anonymous1
Parsing MAF file to classify mutations
Finished Parsing the MAF file to classify mutations
Skipped 272 mutation(s) that are classified as Intron
Skipped 155 mutation(s) that are classified as Silent
Skipped 76 mutation(s) that are classified as IGR
Skipped 43 mutation(s) that are classified as RNA
Skipped 28 mutation(s) that are classified as 5'UTR
Skipped 10 mutation(s) that are classified as 5'Flank
Skipped 8 mutation(s) that are classified as 3'UTR
Skipped 2 mutation(s) that are classified as 3'Flank
Skipped 2 mutation(s) that have unrecognized gene name

Anyone can help?

Answer 1

[Cyriac Kandoth]

My best guess is that your ROI file is using non-UNIX newlines. This could happen if you prepared the ROI file in Windows or OSX. Windows uses "\r\n", and UNIX uses "\n". Since the gene names in the ROI file is at the end of each line, it might be retaining the "\r". You can use a Perl regex to convert Windows newlines to UNIX format:

perl -pe 's/\r\n/\n/g' roi_file_dos > roi_file_unix