SACGF / SACGF/variantgrid

Claire Seurat / combined caller data VCFs

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#312 4 comments 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
VCF
Dominant language
Python
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30
Forks
3
Avg merge
9h 28m
Merged PRs (30d)
42

Description

Claire uploaded some VCFs of type we haven't seen before

https://rollbar.com/jimmy.andrews/VariantGrid/items/2457/?utm_campaign=occurrence_message&utm_medium=slack&utm_source=rollbar-notification
```
VCF Error: Couldn't determine allele depth format field, source: 'combine_caller_data', formats: {'MAX', 'SH', 'SK', 'VC', 'SS', 'SR', 'CB'}
```

Another one failed due to:

https://rollbar.com/jimmy.andrews/VariantGrid/items/2458/?utm_campaign=occurrence_message&utm_medium=slack&utm_source=rollbar-notification
```
UploadPipeline 1493 failed. Filename: VCF Error: null value in column "variant_id" violates not-null constraint
DETAIL: Failing row contains (740278211, U, {-1}, {-1}, null, 729, 0, 0, {-1}, {-1}, {-1}, 0, null).
CONTEXT: COPY snpdb_cohortgenotype_collection_729, line 99: "729,,,0,0,0,U,{-1},{-1},{-1},{-1},{-1}"
```

Will need to hotfix vg.com to get it to upload

https://variantgrid.com/upload/view_upload_pipeline/1493
https://variantgrid.com/upload/view_upload_pipeline/1494

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