Music Bmr Calc-Bmr: error

Question

[Q.S.Yang]

I had installed music by the guide "Installation of the MuSiC suite on unsupported Linux distributions" I am using calcRoiCovg.

the roi file : ensembl_67_cds_ncrna_and_splice_sites_hg19 (download in ubuntu)

calcRoiCovg Sample_n.bam Sample_t.bam roi.file hg19.fa test

Got this error message:

Skipping invalid ROI: 1 11867 12229 DDX11L1

Skipping invalid ROI: 1 12611 12723 DDX11L1

Skipping invalid ROI: 1 13219 14411 DDX11L1

·········

Skipping invalid ROI: Y 28124349 28124468 PRYP4

Skipping invalid ROI: Y 28132779 28132813 PRYP4

Skipping invalid ROI: Y 28133956 28134218 PRYP4

test:

NOTE:

Last line in file shows non-overlapping totals across all ROIs

Gene ROI Length Covered ATs_Covered CGs_Covered CpGs_Covered

NonOverlappingTotals 0 0 0 0

So,where did the error come from and how to fix it? Thanks!

[Chris Miller]

Are you sure that your ROIs match up with your fasta and bam? (i.e. "1" vs "chr1")

[Q.S.Yang]

I solved the error by using a reference fasta that uses the same chromosome names as the ROI file.

Answer 1

[Q.S.Yang]

genome music bmr calc-bmr --bmr-output bmr --roi-file roi_chr.file --gene-mr-file mr_file --reference-sequence hg19.fa --bam-list bam.txt --output-dir rr --maf-file my.maf

my bam.txt

S1 /media/qin//bam/S1b.bam /media/qin/bam/S1a.bam

S2 /media/qin//bam/S2b.bam /media/qin/bam/S2a.bam

my.maf

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   HGVSp_Short Transcript_ID   Exon_Number AF in normal/AF in tumor    AF in tumor t_depth t_ref_count t_alt_count AF in normal    n_depth n_ref_count n_alt_count all_effects Allele  Gene    Feature Feature_type    Consequence cDNA_position   CDS_position    Protein_position    Amino_acids Codons  Existing_variation  ALLELE_NUM  DISTANCE    字段44    SYMBOL  SYMBOL_SOURCE   HGNC_ID BIOTYPE CANONICAL   CCDS    ENSP    SWISSPROT   TREMBL  UNIPARC RefSeq  SIFT    PolyPhen    EXON    INTRON  DOMAINS GMAF    AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF  EA_MAF  CLIN_SIG    SOMATIC PUBMED  MOTIF_NAME  MOTIF_POS   HIGH_INF_POS    MOTIF_SCORE_CHANGE  IMPACT  PICK    VARIANT_CLASS   TSL HGVS_OFFSET PHENO   MINIMISED   ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO  FILTER

rr: gene_covgs dir roi_covgs dir total_covgs

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 249.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 249.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 249.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 250.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 250.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 250.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 250.

Loading per-sample coverages stored in rr/total_covgs

Mismatching number of samples in rr/total_covgs and bam.txt

I did not found the mismatching number of samples in total_coverage and bam.txt.

Answer 2

[Q.S.Yang]

Chromosome names need to match between MAF, ROI file, BAM files, and FASTA file.