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Home Page: https://bcblab.org/espresso-caller
License: MIT License
Automated and reproducible tool for identifying genomic variants at scale ☕️
Home Page: https://bcblab.org/espresso-caller
License: MIT License
When processing new data with pre-processed raw gVCF files, add prefix to sample names through --prefix
ls new_raw_data
100_1.fastq.gz 100_2.fastq.gz 101_1.fastq.gz 101_2.fastq.gz
ls raw_gvcfs
99.g.vcf.gz 100.gvcf.gz
esperesso all --fastq new_raw_data --vcf raw_gvcfs --prefix GVCFS_ res_dir
Will give:
CHROM .... GVCFS_99 GVCFS_100 100 101
BAM validation workflow are generating files with .validation_.txt
.
We should remove the underscore.
Must be ISO8601 format.
Tasks
Provide all required WDL files in the workflows
data package.
This tool should zip and submit imported WDL files as workflow dependency.
File structure:
A USER ERROR has occurred: Bad input: Found two mappings for the same sample: 25_14
/home/benilton/bioinf/tmp/cromwell-executions/JointGenotyping/44718321-e203-43ce-aba0-bb5c53dc0359/call-ImportGVCFs/shard-1049/inputs/-64135002/725_14.b37.g.vcf.gz
/home/benilton/bioinf/tmp/cromwell-executions/JointGenotyping/44718321-e203-43ce-aba0-bb5c53dc0359/call-ImportGVCFs/shard-1049/inputs/-64135002/325_14.b37.g.vcf.gz
bcftools query -l /home/benilton/bioinf/tmp/cromwell-executions/JointGenotyping/44718321-e203-43ce-aba0-bb5c53dc0359/call-ImportGVCFs/shard-1049/inputs/-64135002/725_14.b37.g.vcf.gz
bcftools query -l /home/benilton/bioinf/tmp/cromwell-executions/JointGenotyping/44718321-e203-43ce-aba0-bb5c53dc0359/call-ImportGVCFs/shard-1049/inputs/-64135002/325_14.b37.g.vcf.gz
Sample name in VCF files is ok.
Wrong names in workflow inputs JSON file, 25_14
twice.
Unmapped BAM (uBAM) files are not useful at this moment.
The ready-analysis BAM files may be useful if their CRAM version are not supported.
Number of samples: 491
Workflow: JointDiscovery
Task: SNPsVariantRecalibratorClassic
[January 11, 2020 11:57:03 AM BRST] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 249.44 minutes.
Runtime.totalMemory()=6417809408
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.ArrayList.<init>(ArrayList.java:152)
at org.broadinstitute.hellbender.engine.FeatureCache.getCachedFeaturesUpToStopPosition(FeatureCache.java:213)
at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:506)
at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:340)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:172)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:124)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:239)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.parseTrainingSets(VariantDataManager.java:386)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addDatum(VariantRecalibrator.java:615)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addVariantDatum(VariantRecalibrator.java:573)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.lambda$consumeQueuedVariants$0(VariantRecalibrator.java:544)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator$$Lambda$79/1042273835.accept(Unknown Source)
at java.util.ArrayList.forEach(ArrayList.java:1249)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.consumeQueuedVariants(VariantRecalibrator.java:544)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.apply(VariantRecalibrator.java:523)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:114)
at org.broadinstitute.hellbender.engine.MultiVariantWalker$$Lambda$77/1808470758.accept(Unknown Source)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:112)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
By default this tool will look for genomic intervals files designed for WGS.
We have to add support for custom intervals file for working with WES data.
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