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Mutect Vcf Output

Hello Everyone,

I just started using muTect to detect somatic mutations in matching tumor normal bam files. I would like to output in VCF format for downstream annovar annotation process. Can anyone suggest how to output MuTect in VCF format

Below is the command I am using currently:

java -Xmx2g -jar muTect-1.0.27783.jar --analysis_type MuTect --reference_sequence hg19.fasta --dbsnp dbsnp_132_b37.leftAligned.vcf --input_file:normal Normal.bam --input_file:tumor Tumor.bam --out example.call_stats.txt --coverage_file example.coverage.wig.txt

Thanks Suz

vcf
• 10,763 views • link
updated by Ram Ram • written by KS KS

Is "--coverage_file example.coverage.wig.txt" input or output parameter ?

• 0 views • link
written by Chirag Nepal Chirag Nepal

1 answer

the latest version of MuTect (ver 1.1.4) downloaded from (http://www.broadinstitute.org/cancer/cga/mutect_download) can generate vcf output with --vcf parameter. hope it helps

• 85 views • link
written by henryvuong henryvuong

Hi,

I am trying to run the latest mutect ver 1.1.4 to generate the output in vcf format but i am running with error. The command am using is

java \
  -Xmx14g \
  -jar /scratch/GT/softwares/mutect/muTect-1.1.4.jar \
  --analysis_type MuTect \
  --reference_sequence /scratch/GT/vdas/test_exome/exome/hg19.fa \
  -B:cosmic,VCF /scratch/GT/softwares/mutect/hg1/hg19_cosmic_v54_120711.vcf \
  -B:dbsnp,VCF /scratch/GT/vdas/test_exome/exome/databases/dbsnp_137.hg19.vcf \
  --input_file:normal /scratch/GT/vdas/pietro/exome_seq/results/N_S8980/N_S8980.realigned.recal.bam \
  --input_file:tumor /scratch/GT/vdas/pietro/exome_seq/results/T_S7998/T_S7998.realigned.recal.bam \
  --vcf /scratch/GT/vdas/pietro/exome_seq/results/mutect/mutect_S_313soma2.vcf \
  --coverage_file /scratch/GT/vdas/pietro/exome_seq/results/mutect/coverage_S_313soma2.wig.txt

Can you please tell me where am getting it wrong for getting a desired output of Mutect in vcf format?

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updated by Ram Ram • written by ivivek_ngs ivivek_ngs

yes it is working fine now with the MuTect (ver 1.1.4)

• 1 views • link
written by ivivek_ngs ivivek_ngs

Hi there,

--coverage_file: This corresponds to input or output parameter? Considering we are inputting two bam files (N/T pair), how did you generate one wig file? Simply by merging two bam files?

--intervals: What input did you give for this ? If I want to run the analysis on genome-wide.

• 0 views • link
updated by Ram Ram • written by Chirag Nepal Chirag Nepal

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