VS-815: Add Support for YNG to VQSR Lite #8206
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8206 +/- ##
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Coverage ? 85.814%
Complexity ? 35456
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Files ? 2194
Lines ? 167015
Branches ? 18002
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Hits ? 143323
Misses ? 17292
Partials ? 6400 |
TODO _ UNDO THAT!!! Added monitoring to JointVcfFiltering.wdl
…han vqs_lod for VQSR Lite vs VQSR Classic
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| @@ -75,15 +78,16 @@ workflow GvsCalculatePrecisionAndSensitivity { | |||
| output_basename = output_sample_basename | |||
| } | |||
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| call Add_AS_MAX_VQSLOD_ToVcf { | |||
| call Add_AS_MAX_VQS_Score_ToVcf { | |||
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is it VQS score? not VQSR? Doesn't the S for "score" ?
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Yeah - This label is very specific to this WDL and I was just looking for a generic term to use for lod and calibration_sensitivity. I'll change it up.
| # I am a comment. | ||
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sorry - this is temp debugging code. A stupid way I use to verify that the WDL I'm about to run in Terra has the change I just pushed. Will be removed shortly.
| # This is a reminder to set the priors back to non-zero in GvsWarpTasks before you merge this PR!! TODO | ||
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Can this be done with a passed argument?
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Yeah, that'd be a good idea. I'm still working with Sam to make sure I run classic in the way he wants in order to remove YNG issues. So if what I've done here isn't the way (which I think is what's happening) I may remove this all - but I will try to parameterize it for future work.
| } | ||
| runtime { | ||
| docker: gatk_docker | ||
| disks: "local-disk " + disk_size + " LOCAL" |
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Interesting thing here - 'LOCAL' calls for SSD in chunks of 375GB https://cloud.google.com/compute/docs/disks/#overview (as I read it). I switched to HDD for cost. I don't think performance took a big hit
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@rsasch I don't believe that CreateFilteringFiles.java is used anywhere else except in GVS. As for JointVcfFiltering.wdl, I really tried to avoid changing it, but the changes I had to make were for memory and disk. At this point the changes are in our branch (ah_var_store) and when we merge with main, we can deal with the PR then. But, I also know there's an updated version of this WDL that we are supposed to update to - that will presumably happen before we merge with main. |
…lThroughYNGInVQSRLite
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