Pipeline Description

Germline workflow

Somatic workflow

Software versions

3rd March 2020 - Present

Trim = Cutadapt v1.18
FastQC = FastQC v0.11.7
Map = BWA mem v0.7.15 and Samtools v1.3.1
Deduplicate = Picard v2.18.2
Metrics = Picard v2.18.2
MultiQC = MultiQC v1.7
BQSR = GATK v4.1.4.1
Call = GATK v4.1.4.1
Joint call = GATK v4.1.4.1
VQSR = GATK v4.1.4.1
Peddy = Peddy v.0.4.1
VEP = Ensembl v95
Denovo = GATK v4.1.4.1 and GATK v4.1.2.1

2018 - 2nd March 2020

We use GATK v4.0.3.0 unless otherwise stated below

Trim = Cutadapt v1.14 and v1.18
FastQC = FastQC v0.11.7
Map = BWA mem v0.7.15 and Samtools v1.3.1
Deduplicate = Picard v2.18.2
Metrics = Picard v2.18.2
MultiQC = MultiQC v1.5 and v1.7
BQSR = GATK v4.0.3.0
Call = GATK v4.0.3.0
Joint call = GATK v4.1.2.0
VQSR = GATK v4.0.3.0
Peddy = Peddy v.0.4.1
VEP = Ensembl v95
Denovo = GATK v4.1.2.0