geneimpacts
geneimpacts copied to clipboard
brentp
prioritize effects of variant annotations from VEP, SnpEff, et al.
Hi Brentp I updated vep to version 111. I create the database with gemini and it gives me various types of warnings Please report this on github with the effect-string...
using VEP v105.0: WARNING: unknown severity for 'T|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||1/13|ENST00000342066.8:c.-21+3G>T|||||||1||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1-3|Ensembl|||||||||||||||' with effect 'splice_donor_region_variant'
When using Ensembl VEP version 105 we get following vcf2db warnings: ``` [2022-07-07T10:19Z] WARNING: unknown severity for 'C|splice_donor_region_variant&intron_variant|LOW|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||8/18|ENST00000327044.7:c.888+4C>G|||||||rs13303056|1||-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||Ensembl||G|G|||||||chr1:g.953778G>C||0.829|0.9135|0.9365|0.9523|0.9172|0.8238|0.9333|0.9321|0.8235|0.9508|0.9351|0.9215|0.9599|0.9413|0.9357|0.9192|0.9599|gnomAD_FIN||||||||||NOC2L:K296int|1&1&4||NOC2L&NM_015658.3&c.888+4C>G|||||INTRON_END:953781&DONOR_ESS:4&DONOR_ISS:4&EXON_END:953892&DONOR_GERP_DIFF:NA&DONOR_ESE:45&MUTANT_DONOR_MES:8.46099459345687&EXON_START:953782&DONOR_ISE:20&BRANCHPOINT_DISTANCE:NA&INTRON_START:953289&DONOR_MES_DIFF:-0.0169218360392236|8.461|-0.017|8.444|splice_donor_region_variant' with effect 'splice_donor_region_variant' [2022-07-07T10:19Z] Please report this on github with the effect-string...
A Gemini user on usegalaxy.eu reported yesterday that gemini's is_exonic column is wrongly populated for SnpEff-annotated composite effects. I think this simple typo here is the reason.
Your module asked me to report the following lines. Is there an explanation to why the severity for these particular consequences create issues? Also, how does your program treat comma...
Created vep_float_field and vep_text_field to support the functional impact annotations from dbNSFP.
