The docker-annotation_table-cwl from genome

docker-annotation_table-cwl's Introduction

# Genome

Genome analysis software from The Genome Institute at Washington University
School of Medicine, funded by the National Human Genome Research Institute.

## Testing

Running tests currently depends on many TGI resources so testing cannot be
performed outside TGI at this time.  Within TGI you can run tests by doing,

    genome-test-env test-tracker prove --lsf --git

This chains the `genome-test-env` and `test-tracker` commands together.  See
`test-tracker prove --help` for its usage.  For example, you may need to pass a
value to the `--git` option if your branch is not setup to track
`origin/master`.

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docker-annotation_table-cwl's Issues

Missing CSQ field causes failures

When a CSQ field is missing in the VCF file the current code uses the prior variants CSQ field and ALT to make the vep hash. Prior to line 90 the csq field should be reset to None, further the alt field will be incorrect whenever the CSQ field is missing.

To test run this command in an interactive docker image:

/usr/bin/python /gscuser/zskidmor/add_annotations_to_table_helper.py /gscmnt/gc2547/griffithlab/ebarnell/cromwell-executions/somatic_exome.cwl/fd0111fb-682d-4468-a544-712241a1d5ca/call-detect_variants/detect_variants.cwl/e5a7fe6c-8f23-4a23-9ead-c78b46a49f75/call-add_vep_fields_to_table/inputs/-1761950843/variants.tsv /gscmnt/gc2547/griffithlab/ebarnell/cromwell-executions/somatic_exome.cwl/fd0111fb-682d-4468-a544-712241a1d5ca/call-detect_variants/detect_variants.cwl/e5a7fe6c-8f23-4a23-9ead-c78b46a49f75/call-add_vep_fields_to_table/inputs/-735762534/annotated_filtered.vcf.gz SYMBOL,Feature,Consequence,HGVSc,HGVSp,PICK /gscmnt/gc2547/griffithlab/zskidmor/

The first field without CSQ is at postion 1358669 on chromsome 1

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