Dockerised GATK pipeline

Dockerised version of Ezequiel Anokian's GATK pipeline for germline variants analysis. For pipeline's details please contact: Ezequiel.Anokian@icr.ac.uk

Packaged tool versions

• Java: 1.8.0_212
• GATK: v3.7-0-gcfedb67
• tabix: 1.7-2
• Picardtools: 2.0.1 (built with htsjdk-2.0.1)
• VerifyBamID: 1.1.2
• samtools: 1.7.1
• R: 3.6.0 (2019-04-26) with packages below:
  • ggplot2: 3.1.1
  • gplots: 3.0.1
  • gsalib: 2.1
  • reshape 0.8.8
  • And their dependencies.

Packaged CWL tool

Parts 1 & 2: bam_to_vcf

It produces various quality metrics from the input BAM, clean the BAM file and fix mate info of it, then recalibrates the BAM and generates a gzip GVCF file from it.

Details of inputs and outputs are in cwl/bam_to_gvcf.json.

Note: Only BAM recalibration and HaplotypCaller support multiple threading, 8 cores should be enough for most of cases. Set a sensible amount of RAM accordingly.

Part 3: joint-genotyping

Performs joint-genotyping of all samples per chromosome using GATK GenotypeGVCFs. Excludes samples in the exclude file, which must be filled in according to the following failing BAM QC metrics:

• Insert size metrics: insert size has to be >= 250 bp.
  • Check in file sample.multiple_metrics.insert_size_metrics, column MEAN_INSERT_SIZE, where READ_GROUP = "".
• GC bias: AT_DROPOUT and GC_DROPOUT must be <= 5%.
  • Check in file sample.multiple_metrics.gc_bias.summary_metrics, columns AT_DROPOUT and GC_DROPOUT, where ACCUMULATION_LEVEL = "Sample".
• Alignment metrics: PCT_PF_READS_ALIGNED has to be >= 95%, and PF_MISMATCH_RATE must be <= 5%.
  • Check in file sample.multiple_metrics.alignment_summary_metrics, columns PCT_PF_READS_ALIGNED and PF_MISMATCH_RATE, where CATEGORY != "UNPAIRED".
• Coverage: percentage of genome with at least 20X coverage must be >= 80%.
  • Check in file sample.wgs_metrics.txt, column PCT_20X.
• Contamination: sample contamination has to be <= 3%.
  • Check in file sample.VerifyBamID.selfSM, column FREEMIX.

Details of inputs and outputs are in Dockstore.json.