search

eastgenomics / TSO500R

R package for data analysis with CombinedVariantOutput.tsv data
MIT License
1 stars 3 forks source link

Variant consequence parsing removes required variants #1

Open spaul91 opened 2 years ago

spaul91 commented 2 years ago

Issue found with module that causes required variants to be filtered out if they are not in a predetermined set of consequences.

(Raised in Solid Cancer Informatics (TSO500) meeting 25-APR-2022)

spaul91 commented 2 years ago

Change in approach discussed - the optimal approach would be to remove variants with consequences that aren't required.

List shared by solid cancer scientist:

3_prime_UTR_variant 5_prime_UTR_variant downstream_gene_variant intron_variant splice_region_variant:intron_variant splice_region_variant:synonymous_variant synonymous_variant upstream_gene_variant (blank)