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[ADAM-2150] Use interval start as position for Ensembl VEP ANN attributes #2278

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heuermh merged 1 commit into bigdatagenomics:master from heuermh:issue-2150

Oct 26, 2020

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heuermh commented Oct 26, 2020 •

edited

Fixes #2150

From the VCF ANN specification:

cDNA_position / (cDNA_len optional) : Position in cDNA and trancript’s cDNA length (one
based).

CDS_position / (CDS_len optional): Position and number of coding bases (one based includes
START and STOP codons).

Protein_position / (Protein_len optional): Position and number of AA (one based, including START, but not STOP).

Position should be a single value, but Ensembl VEP provides an interval (e.g. 7264-7275).


          Use interval start as position for Ensembl VEP ANN attributes.

4571de3

heuermh added this to the 0.33.0 milestone

heuermh referenced this pull request in dmaziec/cannoli


          Vep vcf output format

AmplabJenkins commented Oct 26, 2020

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3128/
Test PASSed.

heuermh merged commit 2d9f1c8 into bigdatagenomics:master

heuermh deleted the issue-2150 branch

October 26, 2020 21:41

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