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  • id0
    replied
    I was trying to use Oncotator, which takes MAF file as input. What I ended up doing is simply extracting the relevant columns from a VCF file and arranging them in the correct order.
    Code:
    cat file.vcf | \
    awk -F $'\t' 'BEGIN {OFS=FS} {print $1,$2,$2,$4,$5,"","hg19"}' | \
    sed 's/,\([ACGT]\)\t/\t\1/g' | \
    grep -v "#" | \
    awk 'NR==1{print "Chromosome\tStart_Position\tEnd_Position\tReference_Allele\tTumor_Seq_Allele1\tTumor_Seq_Allele2\tNCBI_Build"}1' \
    > file.maf
    It's not perfect, but for the purpose of Oncotator, this was sufficient.

    Leave a comment:


  • Gesseca
    replied
    I have heard of this script, but I heard that it only works on very specific input.

    Leave a comment:


  • m_two
    replied
    Convert VCF (Variant Call Format) into TCGA MAF (Mutation Annotation Format)


    github.com/cbare/vcf2maf‎

    Read in a vcf file outputted by SNPEff. Parse and output the data in tcga maf format

    code.google.com/p/ngs-analysis/source/browse/modules/somatic/vcf2maf.py

    Same question here: www.biostars.org/p/74822/

    Leave a comment:


  • Gesseca
    replied
    vcf to maf

    I am also looking for a tool that will do this, and I was wondering how people usually generate MAF files? Don't you usually need the original alignments (BAM files)?

    I am working with data where I was only given the vcf file and I dont' know if it's possible to generate MAF without bam files or original alignment files.

    Anybody know?

    Leave a comment:


  • gormleymp
    replied
    Convert Variant Call Format to Mutation Annotation Format

    I am also looking for a tool to convert variant call format files (.vcf) to mutation annotation format files.

    There is a python script vcf2maf available on github but this code looks for specific fields in the vcf header that are unique to TCGA .vcf files. When I run this code on my data it errors out due to missing fields.

    Thanks,
    Mike

    Leave a comment:


  • kasthuri
    started a topic VCF to MAF (Mutation Annotation Format)?

    VCF to MAF (Mutation Annotation Format)?



    Can anybody point me to a tool that can convert a vcf file to Mutation Annotation Format (MAF) file?

    That will be great!

    Thanks
    -Kasthuri

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