Search
Question: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
0
gravatar for Ramiro Magno
6 weeks ago by
Ramiro Magno80
CBMR, Faro, Portugal
Ramiro Magno80 wrote:

Hi All,

I have downloaded a Maf file using TCGAbiolinks (version 2.5.9):

maf <- GDCquery_Maf("BRCA", pipelines = "muse", save.csv = TRUE)

Then I tried to load it as a Maf object using the maftools package (version 1.2.30):

BRCA_maf_csv <- "GDCdata/TCGA.BRCA.muse.d9876b23-3e7d-4d7b-bc1b-3b4393cd2afb.DR-7.0.somatic.maf.csv"
tcga_BRCA_maf <- read.maf(maf = BRCA_maf_csv, removeSilent = TRUE, useAll = FALSE)

but I get this unexpected error: 

Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants,  :
  missing required fields from MAF: Chromosome

This is unexpected because

head -n1 TCGA.BRCA.muse.d9876b23-3e7d-4d7b-bc1b-3b4393cd2afb.DR-7.0.somatic.maf.csv

does show that the Chromosome field is present: 

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,t_depth,t_ref_count,t_alt_count,n_depth,n_ref_count,n_alt_count,all_effects,Allele,Gene,Feature,Feature_type,One_Consequence,Consequence,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,ALLELE_NUM,DISTANCE,TRANSCRIPT_STRAND,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_Adj,ExAC_AF_AFR,ExAC_AF_AMR,ExAC_AF_EAS,ExAC_AF_FIN,ExAC_AF_NFE,ExAC_AF_OTH,ExAC_AF_SAS,GENE_PHENO,FILTER,CONTEXT,src_vcf_id,tumor_bam_uuid,normal_bam_uuid,case_id,GDC_FILTER,COSMIC,MC3_Overlap,GDC_Validation_Status
ADD COMMENTlink modified 25 days ago by tiagochst90 • written 6 weeks ago by Ramiro Magno80
1
gravatar for Ramiro Magno
6 weeks ago by
Ramiro Magno80
CBMR, Faro, Portugal
Ramiro Magno80 wrote:

My apologies...

read.maf expects a tab-delimited file and the downloaded MAF file with TCGAbiolinks is CSV.

ADD COMMENTlink written 6 weeks ago by Ramiro Magno80
0
gravatar for tiagochst
25 days ago by
tiagochst90
Brazil
tiagochst90 wrote:

 Instead of the file you can pass the object.

maf <- GDCquery_Maf("BRCA", pipelines = "muse", save.csv = TRUE)
tcga_BRCA_maf <- read.maf(maf = maf, removeSilent = TRUE, useAll = FALSE)

ADD COMMENTlink written 25 days ago by tiagochst90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 148 users visited in the last hour