Problem generating VCFs from MuTect variant caller

Question

[Jordan]

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!

[arno.guille]

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

[poisonAlien]

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.

[Jordan]

Thanks for the help guys!