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Problem generating VCFs from MuTect variant caller

Hi,

I'm having issues generating VCFs from MuTect variant caller.

Here is my command:

java -XX:ParallelGCThreads=4 \
  -Xmx16g \
  -jar muTect-1.1.4.jar \
  --analysis_type MuTect \
  --reference_sequence human_hg19.fa \
  -nt 16 \
  --input_file:normal $BAMs/Normal.bam \
  --input_file:tumor $BAMs/Tumor.bam \
  --vcf $VC/Sample.vcf \
  -log $VC/Sample.log

I'm using the version 1.1.4 of MuTect and running it in java 1.6 environment.

My problem is, it stops running after analyzing the chr2 i.e., the vcf file generated has only output until chr2. The caller keeps running, but no further data is generated after this point. And then it times out.

Does anyone know what I'm doing wrong?

Thanks!

mutect vcf variant-calling
• 3,977 views • link
updated by Ram Ram • written by Jordan Jordan

Maybe the problem is due to the multithreading.

Here is my command:

java -Xmx16g \
  -jar muTect-1.1.4-bin/muTect-1.1.4.jar \
  --analysis_type MuTect \
  --reference_sequence $ref \
  --cosmic $cosmic_file \
  --dbsnp $dbsnp_file \
  --intervals $target_list_file \
  --input_file:normal $normal \
  --input_file:tumor $tumor \
  --out $output_dir/$name.SNP.stats \
  --vcf $output_dir/$name.SNP.vcf
• 0 views • link
updated by Ram Ram • written by arno.guille arno.guille

Yup ! Its multi-threading. It crashes frequently with -nt argument. Its a known issue. Try without. It should work fine, though it takes much more time to finish.

• 0 views • link
updated by Ram Ram • written by poisonAlien poisonAlien

Thanks for the help guys!

• 0 views • link
updated by Ram Ram • written by Jordan Jordan

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