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Downsized reference available here:
`/hot/users/yiyangliu/MoPepGen/Variant/VEP/gencode.aa/gindel/validate/CPCG0256_ENST00000568044.1`
The command I ran:
```
I have no name!@1ffd9bd622bc:/$ moPep…
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```
##fileformat=VCFv4.2
##mopepgen_version=0.0.1
##parser=parseVEP
##reference_index=/data/Index/GRCh38-EBI-GENCODE34
##genome_fasta=
##annotation_gtf=
##source=gsnp
##CHROM=
##INFO=
##INFO…
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A variant annotated with VEP might have multiple transcript annotations. It could be useful information to know which transcript identifier is related to the predicted score.
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README instructions for running VEP with default Ensembl annotation and custom genocde annotation (the only other annotation source currently supported?)
For gencode, run with something like:
`--c…
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continue to comb through issues with mismatches in germline snps. Many cases involving start lost have been resolved!
`/hot/users/yiyangliu/MoPepGen/Variant/VEP/gencode.aa/gsnp/validate/CPCG0100_EN…
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Hello,
A search for "Everything: pombase" retrieves these results:
PomBase
PomBase Motif search
PomBase data slicer
PomBase VEP
PomBase assembly converter
Of these, only the first two …
mah11 updated
2 years ago
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Hi @sigven,
the **INFO** tags ### EXON and the **INTRON** was generated by the **V…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.4
- OS name and version (`lsb_release -ds`): CentOS Linux release 7.8.2003 (Core)
**To Reproduce**
Exact bcbio command you ha…
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there are quite a few of these, would it possible to skip these start lost variants with brute force?
`/hot/users/yiyangliu/MoPepGen/Variant/VEP/gencode.aa/gsnp/validate/CPCG0100_ENST00000229022.9/…
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## Describe the issue
I'm requesting the "variant classification" field in my command, but the output in this field for all my variants is empty, e.g.:
```
#Uploaded_variation VARIANT_CLASS
chr1_3…