Checks if all the genetic data within a set of files appear to come from the same individual by using Picard CrosscheckFingerprints
java -jar cromwell.jar run crosscheckFingerprints.wdl --inputs inputs.json
| Parameter | Value | Description |
|---|---|---|
inputs |
Array[File] | A list of SAM/BAM/VCF files to fingerprint. |
haplotypeMapFileName |
String | The file name that lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. |
| Parameter | Value | Default | Description |
|---|---|---|---|
haplotypeMapDir |
String | "$CROSSCHECKFINGERPRINTS_HAPLOTYPE_MAP_ROOT" | The directory that contains haplotype map files. By default the modulator data directory. |
outputPrefix |
String | "output" | Text to prepend to all output. |
| Parameter | Value | Default | Description |
|---|---|---|---|
runCrosscheckFingerprints.crosscheckBy |
String | "READGROUP" | Specificies which data-type should be used as the basic comparison unit. Fingerprints from readgroups can be 'rolled-up' to the LIBRARY, SAMPLE, or FILE level before being compared. Fingerprints from VCF can be be compared by SAMPLE or FILE. |
runCrosscheckFingerprints.picardMaxMemMb |
Int | 3000 | Passed to Java -Xmx (in Mb). |
runCrosscheckFingerprints.exitCodeWhenMismatch |
Int | 0 | When one or more mismatches between groups is detected, exit with this value instead of 0. |
runCrosscheckFingerprints.exitCodeWhenNoValidChecks |
Int | 0 | When all LOD score are zero, exit with this value. |
runCrosscheckFingerprints.lodThreshold |
Float | 0.0 | If any two groups (with the same sample name) match with a LOD score lower than the threshold the tool will exit with a non-zero code to indicate error. Program will also exit with an error if it finds two groups with different sample name that match with a LOD score greater than -LOD_THRESHOLD. LOD score 0 means equal likelihood that the groups match vs. come from different individuals, negative LOD score -N, mean 10^N time more likely that the groups are from different individuals, and +N means 10^N times more likely that the groups are from the same individual. |
runCrosscheckFingerprints.validationStringency |
String | "SILENT" | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. See https://jira.oicr.on.ca/browse/GC-8372 for why this is set to SILENT for OICR purposes. |
runCrosscheckFingerprints.modules |
String | "picard/2.21.2 crosscheckfingerprints-haplotype-map/20210201" | Modules to load for this workflow. |
runCrosscheckFingerprints.additionalParameters |
String? | None | Any additional parameters that need to be passed Picard. |
runCrosscheckFingerprints.threads |
Int | 4 | Requested CPU threads. |
runCrosscheckFingerprints.jobMemory |
Int | 6 | Memory (GB) allocated for this job. |
runCrosscheckFingerprints.timeout |
Int | 6 | Number of hours before task timeout. |
| Output | Type | Description |
|---|---|---|
crosscheckMetrics |
File | The crosschecksMetrics file produced by Picard CrosscheckFingerprints |
crosscheckMetricsMatrix |
File | Matrix of LOD scores. This is less informative than the metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Heterozygosity. |
This WDL workflow is wrapped in a Niassa workflow (https://github.com/oicr-gsi/pipedev/tree/master/pipedev-niassa-cromwell-workflow) so that it can used with the Niassa metadata tracking system (https://github.com/oicr-gsi/niassa).
- Building
mvn clean install
- Testing
mvn clean verify \
-Djava_opts="-Xmx1g -XX:+UseG1GC -XX:+UseStringDeduplication" \
-DrunTestThreads=2 \
-DskipITs=false \
-DskipRunITs=false \
-DworkingDirectory=/path/to/tmp/ \
-DschedulingHost=niassa_oozie_host \
-DwebserviceUrl=http://niassa-url:8080 \
-DwebserviceUser=niassa_user \
-DwebservicePassword=niassa_user_password \
-Dcromwell-host=http://cromwell-url:8000
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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