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Old 01-10-2012, 07:39 PM   #1
kasthuri
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Default 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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Old 02-07-2013, 10:40 AM   #2
gormleymp
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Default 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
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Old 09-12-2013, 08:44 AM   #3
Gesseca
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Default 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?
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Old 09-13-2013, 08:17 AM   #4
m_two
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Default

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/
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Old 09-13-2013, 08:26 AM   #5
Gesseca
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Default

I have heard of this script, but I heard that it only works on very specific input.
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Old 09-24-2013, 01:26 PM   #6
id0
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Default

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.
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