Question: Problems running Genome MuSiC Play
2
gravatar for mkaushal
4.2 years ago by
mkaushal100
United States
mkaushal100 wrote:

Hello All,

I am trying to use Genome MuSiC play to get a list of significantly mutated somatic variants. I have normal, primary tumor and metastasized tumor samples from each patient. I have vcfs from Varscan (somatic) and I have converted them to maf using the tool vcf2maf : https://github.com/ckandoth/vcf2maf

I am getting the following error when I tried running MuSiC with one of my samples:

Running genome music proximity...
Could not find required additional columns in um7b_mpileup_varscan_somatic.snpeff.maf
ERROR: Command genome music proximity did not return a true value.

I have checked the maf file specifications here : Are There Any Caveats When Creating A Maf File For Music?. I have the first 34 columns in proper order and also have provided the additional columns required by tools cosmic and proximity after column 34. Here are my column headers:

Hugo_Symbol     Entrez_Gene_Id  Center  NCBI_Build      Chromosome      Start_Position  End_Position    Strand  Variant_Classification  Variant_Type    Reference_Allele      Tumor_Seq_Allele1       Tumor_Seq_Allele2       dbSNP_RS        dbSNP_Val_Status        Tumor_Sample_Barcode    Matched_Norm_Sample_Barcode  Match_Norm_Seq_Allele1   Match_Norm_Seq_Allele2  Tumor_Validation_Allele1        Tumor_Validation_Allele2        Match_Norm_Validation_Allele1   Match_Norm_Validation_Allele2 Verification_Status     Validation_Status       Mutation_Status Sequencing_Phase        Sequence_Source Validation_Method       Score   BAM_File      Sequencer       Tumor_Sample_UUID       Matched_Norm_Sample_UUID        HGVSc   HGVSp   Transcript_ID   transcript_name Exon_Number     t_depth t_ref_count   t_alt_count     n_depth n_ref_count     n_alt_count     all_effects     Effect  Effect_Impact   Functional_Class        Codon_Change    amino_acid_change     Amino_Acid_Length       strand  Gene_Name       Transcript_BioType      Gene_Coding     Transcript_ID   Exon_Rank       Genotype_Number ERRORS  WARNINGS

I am not exactly sure what I am missing here. Can someone please help?

 

 

 

 

music software error • 1.7k views
ADD COMMENTlink modified 4.2 years ago by Cyriac Kandoth5.2k • written 4.2 years ago by mkaushal100
0
gravatar for Cyriac Kandoth
4.2 years ago by
Cyriac Kandoth5.2k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.2k wrote:

I made a mistake in the post "Are There Any Caveats When Creating A Maf File For Music?". Rather than strand, you actually need c_position. So just rename Codon_Change in your MAF to c_position.

Also note that "genome music play" tries to run each tool in the MuSiC suite one-by-one, but it breaks if any of the tools fail. So try running the tools separately starting with bmr calc-covgbmr calc-bmr, smg, pathscan, etc.

ADD COMMENTlink written 4.2 years ago by Cyriac Kandoth5.2k

I took your advice and ran individual modules separately. After some minor hiccups I could finally run the bmr calc-covgbmr calc-bmr and smg . I have a list of smgs now for my samples. I wanted to know if there is a way to correlate the smgs to the sample data? For example this is a gene record from the smg file:

#Gene Indels SNVs Tot Muts Covd Bps Muts pMbp P-value FCPT P-value LRT P-value CT FDR FCPT FDR LRT FDR CT
ERCC5 0 21 21 2058 10204.08 1.04E-11 2.94E-11 9.24E-15 1.53E-08 3.75E-08 1.18E-11

Is there a way to know which samples had variants from ERCC5? Off course I can look into my maf file and figure that out, I was wondering is there some other way out like a summary table?

Thanks a lot for your help.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by mkaushal100
1

The MuSiC suite includes a tool called mutation-relation that looks for significant concurrence or mutual exclusivity of mutated genes. This tool takes a MAF as input, and has an option to save a mutation-matrix-file, a sample-vs-gene matrix. More info down here.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Cyriac Kandoth5.2k

Hi mbhattacharjee

Could you please post your command how you ran the individual modules bmr calc-covgbmr calc-bmr and smg. How did you prepare the data ?

 

I made ROI, maf, and List to run calc-covg, but keep getting error, which i have described here.

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

 

 

 

ADD REPLYlink written 3.5 years ago by Chirag Nepal2.1k
2

Hi,

Commands I used:

#genome music calculate bmr covg step

genome music bmr calc-covg --bam-list tumor_bam_list.txt --output-dir results --reference-sequence hg19.fa  --roi-file hg19_coding_exons_plus10_exclude.bed --cmd-prefix qsub --gene-covg-dir results

#genome music calculate bmr  step
genome music bmr calc-bmr --bam-list tumor_bam_list.txt --maf-file varscan_snp_tumor_edited.maf --output-dir results --reference-sequence hg19.fa --roi-file hg19_coding_exons_plus10_exclude.bed  --bmr-output results --gene-mr-file results

#smg

genome music smg --gene-mr-file results/gene_mrs  --output-file results/smgs_varscan_tumor

Things to remember:

  1. After the final maf files are created change the maf files for running Music:
    1. Are There Any Caveats When Creating A Maf File For Music?
    2. transcript_name column to be inserted after Transcript_ID
    3. change came of column Codon_Change to c_position
    4. change column name of Amino_Acid_Change to amino_acid_change
    5. enter column strand after column Amino_Acid_Length

Note that the column names mentioned above should all be in lower case

2. Prepare a bam list with all bam files

  1. Tab delimited file                            
  2. Format : sample name, normal bam, tumor bam

Make sure all bam index files are also present in respective directories. Make sure there is no extra new lines in the bam list file

3. The ROI file is one based

4. All ref files should be sorted

 

Hops this helps.

 

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by mkaushal100
1

Thanks mbhattacharjee

I am currently running "genome music smg ", and hope it should run without further problem.

Also thanks for the infor "things to remember"

Also plan to upload a detailed tutorial on it.

thanks !

 

ADD REPLYlink written 3.5 years ago by Chirag Nepal2.1k
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