VS-849 - Use the annotation 'AS_MQ' for indels. #8261
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Add monitoring script usage throughout VQSR Classic and Lite.
gbggrant
changed the title
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8261 +/- ##
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Coverage ? 85.873%
Complexity ? 35517
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Files ? 2194
Lines ? 167039
Branches ? 18005
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Hits ? 143442
Misses ? 17216
Partials ? 6381 |
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WDLs failing validation 😿 |
| use_allele_specific_annotations = true, | ||
| monitoring_script = "gs://gvs_quickstart_storage/cromwell_monitoring_script.sh" |
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is this going to work with the Cromwell Local backend test?
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Do you mean our integration test? I modified it to be a parameter to JointVcfFiltering.wdl so that that wdl's cromwell test will work. But now I realize that this might also break our integration tests?
| -resource:hapmap,known=false,training=true,truth=true,prior=0 ~{hapmap_resource_vcf} \ | ||
| -resource:omni,known=false,training=true,truth=true,prior=0 ~{omni_resource_vcf} \ | ||
| -resource:1000G,known=false,training=true,truth=false,prior=0 ~{one_thousand_genomes_resource_vcf} \ | ||
| -resource:dbsnp,known=true,training=false,truth=false,prior=0 ~{dbsnp_resource_vcf} |
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naive question: what do these priors mean here?
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That's temporary - need to do this to use P&S best. I will make a comment - or ideally parameterize this change.
| if [ -s ~{monitoring_script} ]; then | ||
| bash ~{monitoring_script} > monitoring.log & | ||
| fi |
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If this evaluates to false there won't be a monitoring.log but the output is not optional
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Changed this to return a non-optional (zero length file) if no monitoring script is passed.
| if [ -s ~{monitoring_script} ]; then | ||
| bash ~{monitoring_script} > monitoring.log & | ||
| fi |
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Cleaned up and back to just the AS_MQ changes. |
Monitoring script removed.