I used the following command -
pps/jdk/1.6.0_25/bin/java -Xmx2g -jar muTect-1.1.4.jar -T MuTect --reference_sequence /home/exome/repository/ref_genomes/human_g1k_v37.fasta --cosmic $HOME/b37_cosmic_v54_120711.vcf --dbsnp reference_files/dbsnp_132_b37.leftAligned.vcf --input_file:tumor reference_files/S0343/S0343_novoalign.bam --input_file:normal reference_files/S0345/S0345_novoalign.bam --out S0345_S0343.out --vcf S0345_S0343.out.vcf
To produce the mutect vcf output, however no variants were found past chromosome 5. This has also occurred with the other samples I used and is not the case when varscan was used to identify variants. I am not sure why this is happening? If you have a suggestion I would greatly appreciate it. Thank you.