who can give me the data of genome music bmr calc-covg

Question

[qwertyuiop201320142015]

i am a newer of bioinformatics. i have many difficult to solve.Now,i can't find the data of genome music bmr calc-covg.Dose anybody can give me the data .Any help will be appreciate.

[Cyriac Kandoth]

You can use bmr calc-wig-covg if you don't have BAM files. If you are working with TCGA data, wig files are usually available in MAF archives. If you are working on your own data, then you can fake a wig with the expected coverage of the targeting kit you used (e.g. Nimblegen Human Exome, Agilent SureSelect, etc.)

[Chirag Nepal]

Hi Cyriac,

I have been trying to use muSic, but have not been successful yet.

First, I converted vcf to MAF.

vcf2maf.pl --input-vcf P144_vcf.SNPfilter_cov.hc --output-maf P144.maf --tumor-id P144T --normal-i    P144N
vcf2maf.pl --input-vcf P03_vcf.SNPfilter_cov.hc  --output-maf P03.maf --tumor-id P03T --normal-id P    P03N
vcf2maf.pl --input-vcf P07_vcf.SNPfilter_cov.hc  --output-maf P07.maf --tumor-id P07T --normal-id P    P07N

head ROI
chr1    69089    70007    OR4F5
chr1    138531    139311    AL627309.1

head bam-List #The file is tab delimited; The first column name is same as in 16th column in MAF

P144T   /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P144N_SRR1535260_bwa_PCRremoved.bam    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P144T_SRR1535259_bwa_PCRremoved.bam
P03T    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P03N_SRR1535049_bwa_PCRremoved.bam    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P03T_SRR1535048_bwa_PCRremoved.bam
P07T    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P07N_SRR1535055_bwa_PCRremoved.bam    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P07T_SRR1535054_bwa_PCRremoved.bam

genome music bmr calc-covg --gene-covg-dir Test1 --output-dir Test2 --bam-list List --output-dir /NextGenSeqData/project-data/chirag/projects/exomeLiver/music --reference-sequence /tycho-internal/chirag/data/goldenpath/hg19/hg19.fa --roi-file ROI
Tumor BAM for P144   /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P144N_SRR1535260_bwa_PCRremoved.bam not found: ""
Tumor BAM for P03N    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P03N_SRR1535049_bwa_PCRremoved.bam not found: ""
Tumor BAM for P07N    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P07N_SRR1535055_bwa_PCRremoved.bam not found: ""

genome music bmr calc-covg --gene-covg-dir Test1 --output-dir Test2 --bam-list List --output-dir . --reference-sequence /tycho-internal/chirag/data/goldenpath/hg19/hg19.fa --roi-file ROI

Tumor BAM for P144T   /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P144N_SRR1535260_bwa_PCRremoved.bam not found: ""
Tumor BAM for P03T    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P03N_SRR1535049_bwa_PCRremoved.bam not found: ""
Tumor BAM for P07T    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/k

nownDriverKRAS/P07N_SRR1535055_bwa_PCRremoved.bam not found: "

# File is there but keeps giving error, not accessible

du -sh /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P144N_SRR1535260_bwa_PCRremoved.bam
6.1G    /NextGenSeqData/project-data/chirag/rawReadsMapped/shanshanZou_et_al_2015_ica/knownDriverKRAS/P144N_SRR1535260_bwa_PCRremoved.bam

# Options seem to be different in web-page and command line
--maf-file input_dir/myMAF.tsv # This option I did not find in command line, but only saw 
it in webpage

Could you please help me with this?

Thanks for your help!

cheers
Chirag

[Cyriac Kandoth]

In the future, please open a new question. As long as you tag it with appropriate keywords like "music", I will find it. The problem is in your bam-list "List". Make sure that it is tab-delimited, and uses Unix newlines.

[Sean Davis]

calc-covg is something that you generate on your own data, generally. Is that what you want to do?

[Chirag Nepal]

Hi,

If you could post your exact command that you used, it might be useful to other people.