Select AutoPVS1 transcript as final variant annotation

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #144. This PR modifies autogvp and annotation filtering scripts to retain autopvs1 transcript annotation as final outputted annotation for each variant.

What was your approach?

• modified 01-annotate_variants_CAVATICA_input.R and annotate_variants_custom_input.R to retain autopvs1 Feature column.
• modified 04-filter_gene_annotations.R to filter annotated vcf for only vcf_id-Feature pairs in autogvp output.

What GitHub issue does your pull request address?

#144

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please run shell script on both pbta and custom test files

bash run_autogvp.sh --workflow="cavatica" \
--vcf=input/test_pbta.single.vqsr.filtered.vep_105.vcf \
--filter_criteria='INFO/AF>=0.2 INFO/DP>=15 (gnomad_3_1_1_AF_non_cancer<0.01|gnomad_3_1_1_AF_non_cancer=".")' \
--intervar=input/test_pbta.hg38_multianno.txt.intervar \
--multianno=input/test_pbta.hg38_multianno.txt \
--autopvs1=input/test_pbta.autopvs1.tsv \
--outdir=../results \
--out="test_pbta"

bash run_autogvp.sh --workflow="custom" \
--vcf=input/test_VEP.vcf \
--clinvar=input/clinvar.vcf.gz \
--intervar=input/test_VEP.hg38_multianno.txt.intervar \
--multianno=input/test_VEP.vcf.hg38_multianno.txt \
--autopvs1=input/test_autopvs1.txt \
--outdir=../results \
--out="test_custom"

Is there anything that you want to discuss further?

There are rare instances (I believe only in the custom test files) in which variants are annotated as intergenic by VEP, but have transcript annotation by AutoPVS1. This results in NA annotation columns for these variants in the final output, since the AutoPVS1 transcript is not found in the VEP vcf file. I will plan to run this on larger data sets to determine if this only happens with intergenic variants, in which case we can annotate them as such in the final output.

Documentation Checklist

• The function has examples to showcase the usage

[naqvia]

The logic and code looks good to me. Runs as expected. I appreciate your usage of glue::glue and I like the idea of using an input file output_colnames.tsv. I am assuming this would be the default version and will eventually allow the user to define their own file? Not crucial at the moment, but If the latter, we'd prob need to amend the readme!

[rjcorb]

hmm good point...I suppose we could add instructions for modifying output_colnames, it's pretty comprehensive now but there may be other annotations we're not capturing here