I used Mutect for my normal/tumor pair samples(exome) with the bam files which are preprocessed by GATK for BQSR and those recalibrated bam files are used for Mutect downstream for somatic mutation identification. To note during processing of bam in GATK I have already used target bed files provided by the company which are used for target enrichment during the library preparation process. Still I wanted to see if I use those target bed files again with Mutect do I get mutations with better annotation on exomes or not. When I run mutect without the --intervals option i.e not specifying the Target enrichment bed files I get variants which around 1800 which are having the flag KEEP but when use the option --intervals with MuTect 1.1.4 with I do not get any variants with flag KEEP and COVERED. Is it not a right way to use the target bed file of the company while running the MuTect on GATK processed bam files? The command line I used is below
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 --cosmic /data/PGP/exome/mutect/hg19/hg19_cosmic_v54_120711.vcf --dbsnp /scratch/GT/vdas/test_exome/exome/databases/dbsnp_137.hg19.vcf --input_file:normal /scratch/GT/vdas/pietro/exome_seq/results/N_S8981/N_S8981.realigned.recal.bam --input_file:tumor /scratch/GT/vdas/pietro/exome_seq/results/T_S7999/T_S7999.realigned.recal.bam --out /scratch/GT/vdas/pietro/exome_seq/results/mutect/param_test/mutect_S_333soma_t.txt --coverage_file /scratch/GT/vdas/pietro/exome_seq/results/mutect/param_test/LG.coverage.wig.txt --vcf /scratch/GT/vdas/pietro/exome_seq/results/mutect/param_test/mutect_S_333soma_t.vcf --intervals /scratch/GT/vdas/referenceBed/hg19/ss_v4/SureSelect_XT_Human_All_Exon_V4.bed --fraction_contamination 0.5
I would like to know if anyone has tried this or not and the feedback. Is it advisable to use the target bed files with --interval options of GATK recalibrated bam files while running MuTect and fishing out somatic mutations for the pair?