You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am observing that the annotated VCF output contains "p.(%3D)" instead of "p.(=)"... I am not sure if this is a local issue, but unfortunately I currently have only access to a single Linux server and insufficient admin privileges to install jannovar anywhere else.
chr1 98039419 rs56038477 C T 433 PASS ANN=T|synonymous_variant|LOW|DPYD|1806|transcript|NM_000110.3|Coding|11/23|c.1236G>A|p.(%3D)|1373/843317|1236/3078|412/1026||;EXON;FC=Synonymous_E412E;GI=DPYD;SNVHPOL=2;SNVSB=-39.6;TI=NM_000110 GT:GQ:GQX:DP:DPF:AD 0/1:466:35:157:13:83,74
Expected behavior
jannovar annotate-pos -d ~/Analysis/resources/refs/data/hg19/refseq/refseq_curated_105_hg19.ser -c 'chr1:98039419C>T'
Options
JannovarAnnotatePosOptions [genomicChanges=[chr1:98039419C>T], toString()=JannovarAnnotationOptions [useThreeLetterAminoAcidCode=false, nt3PrimeShifting=false, showAll=false, databaseFilePath=/home/skurscheid/Analysis/resources/refs/data/hg19/refseq/refseq_curated_105_hg19.ser, toString()=JannovarBaseOptions [reportProgress=true, httpProxy=null, httpsProxy=null, ftpProxy=null, verbosity=1]]]
Deserializing transcripts...
INFO Deserializing JannovarData from /home/skurscheid/Analysis/resources/refs/data/hg19/refseq/refseq_curated_105_hg19.ser
INFO Deserialization took 4.13 sec.
#change effect hgvs_annotation messages
chr1:98039419C>T SYNONYMOUS_VARIANT DPYD:NM_000110.3:c.1236G>A:p.(=) ..
Describe the bug
Hi there,
I am observing that the annotated VCF output contains "p.(%3D)" instead of "p.(=)"... I am not sure if this is a local issue, but unfortunately I currently have only access to a single Linux server and insufficient admin privileges to install jannovar anywhere else.
I am using jannovar v0.36 installed via conda.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
Additional information
The text was updated successfully, but these errors were encountered: