oicr-gsi/sample-fingerprinting

workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

fingerprintCollector

FingerprintCollector 2.1, workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

Overview

Fingerprint Collector workflow produces "fingerprint" data for input alignments passed as .bam files. It is a part of the original implementation and its task is to produce all intermediate data just before creation of similarity matrix and sample swap report. The goal is to decrease the stress on the system by splitting the workflow and collecting variation data independently for each input .bam file. The below graph describes the process:

Dependencies

• gatk 4.1.7.0, gatk 3.6.0
• tabix 0.2.6
• python 3.6

Usage

Cromwell

java -jar cromwell.jar run fingerprintCollector.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
inputBam	File	Input lane-level BAM file
inputBai	File	Index for the input BAM file
refFasta	String	Path to the reference fasta file
hotspotSNPs	String	Path to the gzipped hotspot vcf file
runHaplotypeCaller.modules	String	Names and versions of modules
runDepthOfCoverage.modules	String	Names and versions of modules
runFinCreator.modules	String	Names and versions of modules

Optional workflow parameters:

Parameter	Value	Default	Description
outputFileNamePrefix	String	basename(inputBam,".bam")	Output prefix, customizable. Default is the input file's basename.

Optional task parameters:

Parameter	Value	Default	Description
runHaplotypeCaller.jobMemory	Int	8	memory allocated for Job
runHaplotypeCaller.timeout	Int	24	Timeout in hours, needed to override imposed limits
runHaplotypeCaller.stdCC	Float	30.0	standard call confidence score, default is 30
runDepthOfCoverage.jobMemory	Int	8	memory allocated for Job
runDepthOfCoverage.timeout	Int	24	Timeout in hours, needed to override imposed limits
runFinCreator.chroms	Array[String]	["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX"]	Canonical chromosomes in desired order (used for soting lines in .fin file)
runFinCreator.timeout	Int	10	Timeout in hours, needed to override imposed limits
runFinCreator.jobMemory	Int	8	memory allocated for Job

Outputs

Output	Type	Description
outputVcf	File	gzipped vcf expression levels for all genes recorded in the reference
outbutTbi	File	expression levels for all isoforms recorded in the reference
outputFin	File	Custom format file, shows which hotspots were called as variants

Commands

This section lists command(s) run by fingerprintCollector workflow

• Running fingerprintCollector

GATK Haplotype Caller using a list of genotyping hotspots:

 gatk HaplotypeCaller
     -R REF_FASTA
     -I INPUT_BAM
     -O SAMPLE_ID.snps.raw.vcf
    --read-filter CigarContainsNoNOperator
    --stand-call-conf STD_CC
     -L HOTSPOT_SNPS

 bgzip -c SAMPLE_ID.snps.raw.vcf > SAMPLE_ID.snps.raw.vcf.gz
 tabix -p vcf SAMPLE_ID.snps.raw.vcf.gz 

```

Depth of Coverage analysis:

```
 java -jar GenomeAnalysisTK.jar 
      -R REF_FASTA
      -T DepthOfCoverage
      -I INPUT_BAM
      -o SAMPLE_ID
      -filterRNC
      -L HOTSPOT_SNPS 

```

Creation of a fingerprint file:

...

 Custom python code producing .fin file with hotspot calls

 please refer to the fingerprintCollector.wdl for source

```
## Support

For support, please file an issue on the [Github project](https://github.com/oicr-gsi) or send an email to [email protected] .

_Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)_