VariantCaller_GATK3.6
Version 1

Stable

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container orchestration platform.

This demonstrator will be aligned with the current implementation study on Development of Architecture for Software Containers at ELIXIR and its use by EXCELERATE use-case communities

For this implementation, different steps are required:

  1. Adapt the pipeline to CWL and dockerise elements

  2. Align with IS efforts on software containers to package the different components (Nextflow)

  3. Submit trio of Illumina NA12878 Platinum Genome or Exome to the GA4GH platform cloud (by Aspera or ftp server)

  4. Run the RD-Connect pipeline on the container platform

  5. Return corresponding gvcf files

  6. OPTIONAL: annotate and update to RD-Connect playground instance

N.B: The demonstrator might have some manual steps, which will not be in production.

RD-Connect pipeline

Detailed information about the RD-Connect pipeline can be found in Laurie et al., 2016

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The applications

1. Name of the application: Adaptor removal

Function: remove sequencing adaptors

Container (readiness status, location, version): cutadapt (v.1.18)

Required resources in cores and RAM: current container size 169MB

Input data (amount, format, directory..): raw fastq

Output data: paired fastq without adaptors

2. Name of the application: Mapping and bam sorting

Function: align data to reference genome

Container : bwa-mem (v.0.7.17) / Sambamba (v. 0.6.8 )(or samtools)

Resources :current container size 111MB / 32MB

Input data: paired fastq without adaptors

Output data: sorted bam

3. Name of the application: MarkDuplicates

Function: Mark (and remove) duplicates

Container: Picard (v.2.18.25)

Resources: current container size 261MB

Input data:sorted bam

Output data: Sorted bam with marked (or removed) duplicates

4. Name of the application: Base quality recalibration (BQSR)

Function: Base quality recalibration

Container: GATK (v.3.6-0)

Resources: current container size 270MB

Input data: Sorted bam with marked (or removed) duplicates

Output data: Sorted bam with marked duplicates & base quality recalculated

5. Name of the application: Variant calling

Function: variant calling

Container: GATK (v.3.6-0)

Resources: current container size 270MB

Input data:Sorted bam with marked duplicates & base quality recalculated

Output data: unannotated gvcf per sample

6. (OPTIONAL)Name of the application: Quality of the fastq

Function: report on the sequencing quality

Container: fastqc 0.11.8

Resources: current container size 173MB

Input data: raw fastq

Output data: QC report

Licensing

GATK declares that archived packages are made available for free to academic researchers under a limited license for non-commercial use. If you need to use one of these packages for commercial use. https://software.broadinstitute.org/gatk/download/archive

Inputs

ID Name Description Type
fastq_files n/a List of paired-end input FASTQ files File[]
reference_genome n/a Compress FASTA files with the reference genome chromosomes File[]
known_indels_file n/a VCF file correlated to reference genome assembly with known indels File
known_sites_file n/a VCF file correlated to reference genome assembly with know sites (for instance dbSNP) File
chromosome n/a Label of the chromosome to be used for the analysis. By default all the chromosomes are used string
readgroup_str n/a Parsing header which should correlate to FASTQ files string
sample_name n/a Sample name string
gqb n/a Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order) int[]

Steps

ID Name Description
unzipped_known_sites
unzipped_known_indels
gunzip
picard_dictionary
cutadapt2
bwa_index
samtools_index
bwa_mem
samtools_sort
picard_markduplicates picard-MD
gatk3-rtc gatk3-rtc
gatk-ir gatk-ir
gatk-base_recalibration gatk-base_recalibration
gatk-base_recalibration_print_reads gatk-base_recalibration_print_reads
gatk_haplotype_caller gatk-haplotype_caller

Outputs

ID Name Description Type
metrics n/a Several metrics about the result File
gvcf n/a unannotated gVCF output file from the mapping and variant calling pipeline File
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Views: 41   Downloads: 1

Created: 18th Feb 2021 at 15:01

Last updated: 19th Feb 2021 at 12:13

Last used: 25th Feb 2021 at 11:46

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Version 1 Created 18th Feb 2021 at 15:01 by Laura Rodriguez-Navas

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