Whole Genome Sequencing (MUTECT)

FASTQC

omics_pipe.modules.fastqc.fastqc(sample, fastqc_flag)

QC check of raw .fastq files using FASTQC.

input:

.fastq file

output:

folder and zipped folder containing html, txt and image files

citation:

Babraham Bioinformatics

link:

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

parameters from parameters file:

RAW_DATA_DIR:

QC_PATH:

FASTQC_VERSION:

COMPRESSION:

BWA-MEM

omics_pipe.modules.bwa.bwa_mem(sample, bwa_mem_flag)

BWA aligner with BWA-MEM algorithm.

input:

.fastq

output:

.sam

citation:

Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]

link:

http://bio-bwa.sourceforge.net/bwa.shtml

parameters from parameters file:

BWA_RESULTS:

TEMP_DIR:

SAMTOOLS_VERSION:

BWA_VERSION:

GENOME:

RAW_DATA_DIR:

BWA_OPTIONS:

COMPRESSION:

MUTECT

omics_pipe.modules.mutect.mutect(sample, mutect_flag)

Runs MuTect on paired tumor/normal samples to detect somatic point mutations in cancer genomes.

input:

.bam

output:

call_stats.txt

citation:

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnology (2013).doi:10.1038/nbt.2514

link:

http://www.broadinstitute.org/cancer/cga/mutect

parameters from parameters file:

BWA_RESULTS:

TEMP_DIR:

GATK_VERSION:

GENOME:

DBSNP:

MILLS:

G1000:

CAPTURE_KIT_BED: