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:
Picard tools Mark Duplicates.
BWA_RESULTS:
TEMP_DIR:
PICARD_VERSION:
SAMTOOLS_VERSION:
GATK preprocessing steps for whole exome sequencing.
BWA_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
MILLS:
G1000:
CAPTURE_KIT_BED:
GATK preprocessing steps for whole genome sequencing.
BWA_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
MILLS:
G1000:
GATK_variant_discovery.
BWA_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
GATK_variant_filtering.
BWA_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
MILLS_G1000:
OMNI:
HAPMAP: