https://github.com/oicr-gsi/sample-fingerprinting
workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow
https://github.com/oicr-gsi/sample-fingerprinting
fingerprinting genotyping qc reporting variant-calling workflow
Last synced: 2 months ago
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workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow
- Host: GitHub
- URL: https://github.com/oicr-gsi/sample-fingerprinting
- Owner: oicr-gsi
- Created: 2015-07-08T19:55:00.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2025-09-11T13:58:01.000Z (9 months ago)
- Last Synced: 2025-09-11T16:37:31.621Z (9 months ago)
- Topics: fingerprinting, genotyping, qc, reporting, variant-calling, workflow
- Language: WDL
- Homepage:
- Size: 1.18 MB
- Stars: 0
- Watchers: 15
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
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README
# 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](https://gatk.broadinstitute.org)
* [tabix 0.2.6](http://www.htslib.org)
* [python 3.6](https://www.python.org/)
## 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 | Labels
---|---|---|---
`outputVcf`|File|gzipped vcf expression levels for all genes recorded in the reference|vidarr_label: outputVcf
`outbutTbi`|File|expression levels for all isoforms recorded in the reference|vidarr_label: outbutTbi
`outputFin`|File|Custom format file, shows which hotspots were called as variants|vidarr_label: outputFin
## 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 gsi@oicr.on.ca .
_Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)_