QC check of raw .fastq files using FASTQC.
RAW_DATA_DIR:
QC_PATH:
FASTQC_VERSION:
COMPRESSION:
BWA aligner with BWA-MEM algorithm.
BWA_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BWA_VERSION:
GENOME:
RAW_DATA_DIR:
BWA_OPTIONS:
COMPRESSION:
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:
SAMTOOLS_VERSION:
GATK preprocessing steps for whole genome sequencing.
BWA_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
MILLS:
G1000:
SAMTOOLS_VERSION:
GATK_variant_discovery.
BWA_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
VARIANT_RESULTS:
GATK_variant_filtering.
VARIANT_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
MILLS:
OMNI:
HAPMAP:
R_VERSION:
G1000_SNPs:
G1000_Indels:
GATK_variant_filtering.
parameters from parameters file:
VARIANT_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
MILLS_G1000:
OMNI:
HAPMAP:
R_VERSION:
G1000: