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Question: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
0
gravatar for Ramiro Magno
12 months ago by
Ramiro Magno100
CBMR, Faro, Portugal
Ramiro Magno100 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 11 months ago by tiagochst100 • written 12 months ago by Ramiro Magno100
1
gravatar for Ramiro Magno
12 months ago by
Ramiro Magno100
CBMR, Faro, Portugal
Ramiro Magno100 wrote:

My apologies...

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

ADD COMMENTlink written 12 months ago by Ramiro Magno100
0
gravatar for tiagochst
11 months ago by
tiagochst100
Brazil
tiagochst100 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 11 months ago by tiagochst100
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