crosscheckFingerprintCaller

To call sequencing library swaps and matches from CrosscheckFingerprints output given OICR metadata.

Overview

Dependencies

• crosscheck_fingerprint_caller
• jq

Usage

Cromwell

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

Inputs

Required workflow parameters:

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.
metadata	Array[Map[String,String]]	Metadata to add to the CrosscheckFingerprints data
ambiguous	Array[Map[String,String]]	The ambiguous LOD ranges for each library design pair
outputFileNamePrefix	String	String to add to the output file names

Optional workflow parameters:

Parameter	Value	Default	Description
compareAgainst	Array[String]?	None	If defined, inputs are compared against these files. Ignored if cachedFilePath is defined.
cachedFilePath	String?	None	Previous output of this workflow. If given, only new comparisons will be calculated.
haplotypeMapDir	String	"$CROSSCHECKFINGERPRINTS_HAPLOTYPE_MAP_ROOT"	The directory that contains haplotype map files. By default the modulator data directory.
crosscheckBy	String	"SAMPLE"	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.
calculateTumorAwareResults	Boolean	false	Specifies whether the Tumor-aware result should be calculated. These are time consuming and can roughly double the runtime of the tool. When crosschecking many groups not calculating the tumor-aware results can result in a significant speedup.
seperator	String	";"	Which character is used to seperate multiple batches

Optional task parameters:

Parameter	Value	Default	Description
crosscheckFingerprints.createNewCrosscheckFingerprints_timeout	Int	1	Number of hours before task timeout.
crosscheckFingerprints.createNewCrosscheckFingerprints_jobMemory	Int	1	Memory (GB) allocated for this job.
crosscheckFingerprints.createNewCrosscheckFingerprints_threads	Int	1	Requested CPU threads.
crosscheckFingerprints.runCachedInverse_timeout	Int	6	Number of hours before task timeout.
crosscheckFingerprints.runCachedInverse_jobMemory	Int	6	Memory (GB) allocated for this job.
crosscheckFingerprints.runCachedInverse_threads	Int	4	Requested CPU threads.
crosscheckFingerprints.runCachedInverse_modules	String	"picard/3.1.0 crosscheckfingerprints-haplotype-map/20230324"	Modules to load for this workflow.
crosscheckFingerprints.runCachedInverse_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.
crosscheckFingerprints.runCachedInverse_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.
crosscheckFingerprints.runCachedInverse_exitCodeWhenNoValidChecks	Int	0	When all LOD score are zero, exit with this value.
crosscheckFingerprints.runCachedInverse_exitCodeWhenMismatch	Int	0	When one or more mismatches between groups is detected, exit with this value instead of 0.
crosscheckFingerprints.runCachedInverse_picardMaxMemMb	Int	3000	Passed to Java -Xmx (in Mb).
crosscheckFingerprints.runCached_timeout	Int	6	Number of hours before task timeout.
crosscheckFingerprints.runCached_jobMemory	Int	6	Memory (GB) allocated for this job.
crosscheckFingerprints.runCached_threads	Int	4	Requested CPU threads.
crosscheckFingerprints.runCached_modules	String	"picard/3.1.0 crosscheckfingerprints-haplotype-map/20230324"	Modules to load for this workflow.
crosscheckFingerprints.runCached_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.
crosscheckFingerprints.runCached_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.
crosscheckFingerprints.runCached_exitCodeWhenNoValidChecks	Int	0	When all LOD score are zero, exit with this value.
crosscheckFingerprints.runCached_exitCodeWhenMismatch	Int	0	When one or more mismatches between groups is detected, exit with this value instead of 0.
crosscheckFingerprints.runCached_picardMaxMemMb	Int	3000	Passed to Java -Xmx (in Mb).
crosscheckFingerprints.usePowerOfCache_timeout	Int	1	Number of hours before task timeout.
crosscheckFingerprints.usePowerOfCache_jobMemory	Int	1	Memory (GB) allocated for this job.
crosscheckFingerprints.usePowerOfCache_threads	Int	1	Requested CPU threads.
crosscheckFingerprints.runCrosscheckFingerprints_timeout	Int	6	Number of hours before task timeout.
crosscheckFingerprints.runCrosscheckFingerprints_jobMemory	Int	6	Memory (GB) allocated for this job.
crosscheckFingerprints.runCrosscheckFingerprints_threads	Int	4	Requested CPU threads.
crosscheckFingerprints.runCrosscheckFingerprints_modules	String	"picard/3.1.0 crosscheckfingerprints-haplotype-map/20230324"	Modules to load for this workflow.
crosscheckFingerprints.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.
crosscheckFingerprints.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.
crosscheckFingerprints.runCrosscheckFingerprints_exitCodeWhenNoValidChecks	Int	0	When all LOD score are zero, exit with this value.
crosscheckFingerprints.runCrosscheckFingerprints_exitCodeWhenMismatch	Int	0	When one or more mismatches between groups is detected, exit with this value instead of 0.
crosscheckFingerprints.runCrosscheckFingerprints_picardMaxMemMb	Int	3000	Passed to Java -Xmx (in Mb).
crosscheckFingerprints.compareAgainstFile_timeout	Int	1	Number of hours before task timeout.
crosscheckFingerprints.compareAgainstFile_jobMemory	Int	1	Memory (GB) allocated for this job.
crosscheckFingerprints.compareAgainstFile_threads	Int	1	Requested CPU threads.
crosscheckFingerprints.inputsToFile_timeout	Int	1	Number of hours before task timeout.
crosscheckFingerprints.inputsToFile_jobMemory	Int	1	Memory (GB) allocated for this job.
crosscheckFingerprints.inputsToFile_threads	Int	1	Requested CPU threads.
writeAmbiguousRange.timeout	Int	1	The hours until the task is killed.
writeAmbiguousRange.memory	Int	1	The GB of memory provided to the task.
writeAmbiguousRange.threads	Int	1	The number of threads the task has access to.
writeAmbiguousRange.modules	String	"jq/1.6"	The modules that will be loaded.
writeMetadata.timeout	Int	1	The hours until the task is killed.
writeMetadata.memory	Int	1	The GB of memory provided to the task.
writeMetadata.threads	Int	1	The number of threads the task has access to.
writeMetadata.modules	String	"jq/1.6"	The modules that will be loaded.
runMain.timeout	Int	1	The hours until the task is killed.
runMain.memory	Int	1	The GB of memory provided to the task.
runMain.threads	Int	1	The number of threads the task has access to.
runMain.modules	String	"crosscheck-fingerprint-caller/1.0.0"	The modules that will be loaded.

Outputs

Output	Type	Description	Labels
calls	File	CSV file with metadata and swap calls for each library	vidarr_label: calls
detailed	File	CSV file with metadata and detailed swap calls for each library pair	vidarr_label: detailed

Commands

See WDL

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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