Tool:Mutect: Accurate Identification Of Somatic Point Mutations

Question

[zx8754]

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

MuTect link

[ivivek_ngs]

I would like to ask if there is any possibility to retrieve Mutect output in vcf format? I am trying to do that but to no avail. I am using Mutect for the first time for my exome data normal /tumor pair and now I have retrieved around 1800 novel variations for my pair, I want to know if any additional downstream filtering can be applied or not then I would like to apply them to get more HC ones and then annotate them. I am confident of annotating them with ANNOVAR but I feel ANNOVAR is not complete and that is the reason I want to annotate with snpEFF wihch sadly does not let you annotate in .txt format anymore. So can you please tell me how to get the output in VCF format from mutect?

Thanks

Answer 1

[ivivek_ngs]

@zx8754

Yes please find the below code, This should work. Let me know if you face any problems, It works for the mutect file which are filtered first for just KEEP and COVERED so that you get a out.txt of mutect with only high confidence variants and then convert it to the vcf format.

#!/usr/bin/python

import sys
text=open(sys.argv[1]).readlines()
text=filter(lambda x:x.split('\t')[31].strip()=='KEEP',text)
text=map(lambda x:x.split('\t')[0]+'\t'+x.split('\t')[1]+'\t.\t'+x.split('\t')[2]+'\t'+x.split('\t')[3]+'\t.\tPASS\t.\n',text)
file=open(sys.argv[1].replace('.txt','.vcf'),'w')

file.write('##fileformat=VCFv4.0\n')
file.write('##source=dbSNP\n')
file.write('##dbSNP_BUILD_ID=137\n')
file.write('##reference=hg19\n')
file.write('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n')

for i in text:
        file.write(i)
file.close()

Answer 2

[mmterpstra]

You might also look at: https://github.com/broadinstitute/mutect

Last I checked (~6months ago) the github page hosted the most recent version of mutect. Also with adding the vcf format output

[ivivek_ngs]

Thanks for the input. I managed to write a script to convert my text to vcf format.

[zx8754]

Do you mind sharing?