QC check of raw .fastq files using FASTQC.
RAW_DATA_DIR:
QC_PATH:
FASTQC_VERSION:
BWA aligner with BWA-MEM algorithm.
BWA_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BWA_VERSION:
GENOME:
RAW_DATA_DIR:
BWA_OPTIONS:
Runs MuTect on paired tumor/normal samples to detect somatic point mutations in cancer genomes.
BWA_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
MILLS:
G1000:
CAPTURE_KIT_BED: