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neksa / mutagene

Python library and package for mutational analysis
https://www.ncbi.nlm.nih.gov/projects/mutagene/
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MAF parsing error #1

Closed neksa closed 5 years ago

neksa commented 5 years ago

Error parsing MAF file

  1. MutaGen requires Codon_Change or Codons fields in MAF files
  2. Could not find HGVSp_Short or Protein_Change fields in MAF file

Reproduce:

$ mutagene rank -i test.maf -g hg38 -o ranking.txt -c pancancer
WARNING MAF format not recognized
WARNING No mutations to rank

Sample:

Hugo_Symbol     Entrez_Gene_Id   Center   NCBI_Build        Chromosome     Start_Position     End_Position           Strand   Variant_Classification       tumor_VAF        Variant_Type      Reference_Allele  Tumor_Seq_Allele1           Tumor_Seq_Allele2          dbSNP_RS         Tumor_Sample_Barcode   Mutation_Status AAChange           Transcript_Id      TxChange          GeneDetail.refGene
SAMD11           NCC     hg38     chr1     930314  930314  +         Missense_Mutation        0.5       SNP      C           C         T                    NSLA_475_exonic_anno.txt           Somatic p.H78Y  NM_152486       c.C232T 
...
neksa commented 5 years ago

Suggested solution: considering AAChange column, and I can try to infer codon information from TxChange