MAFTOOLS HELP - Mutational Signature

Question

[David_emir]

Hi All,

I am trying to run mutational signatures on my MAF file, using maftools (https://github.com/PoisonAlien/maftools). while trying to run this i am constantly My the following error. It would be great if you can help me. My knowledge in this area is elementary level.

I am using Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa as my reference file. It would be of a GREAT HELP if you can help me sorting out this issue.

Please let me know the solution for this roadblock !!! Error as follows!!!

contigs in maf: [1] "chr10" "chr12" "chr22" "chr3" "chr1" "chr2" "chr4" "chr9" "chr7" [10] "chr16" "chr17" "chr19" "chr6" "chr13" "chr11" "chr20" "chr18" "chr5" [19] "chr14" "chr15" "chrX" "chr8" "chr21" "chrY" missing reference contigs from fasta file. [1] "chr10" "chr12" "chr22" "chr3" "chr1" "chr2" "chr4" "chr9" "chr7" [10] "chr16" "chr17" "chr19" "chr6" "chr13" "chr11" "chr20" "chr18" "chr5" [19] "chr14" "chr15" "chrX" "chr8" "chr21" "chrY"

Contig names in MAF must match to contig names in reference fasta. Ignorinig 29573 single nucleotide variants from chr10, chr12, chr22, chr3, chr1, chr2, chr4, chr9, chr7, chr16, chr17, chr19, chr6, chr13, chr11, chr20, chr18, chr5, chr14, chr15, chrX, chr8, chr21, chrY

Error in trinucleotideMatrix(maf = laml, ref_genome = "/home//mutation/centos/gr37.fasta", : Zero mutations to analyze! Maybe add or remove prefix?

Thanks a lot, Dav

Answer 1

[shubhra.bhattacharya]

Hey!

Please check whether the chromosomal naming nomenclature matches of the reference matches with the input file. Such as that your reference has chromosome named as chr10,chr1 etc. I guess chromosomes are named as 1 ,2 and so on in the reference.