Dave Lawrence
Dave Lawrence
## Checklist Put an `x` in the bracket when you have completed each task, like this: `[x]` - [ X] This issue is not about installing previous versions of django-smart-selects...
I have been [told by Ensembl](https://github.com/Ensembl/ensembl-vep/issues/1053#issuecomment-924650545) that: > Ensembl transcripts completely match the reference genome they are annotated against, so HGVS transcript level variant descriptions will be mapped to the...
The following VCF contains 3 deletions of length 1kb, 2kb and 3kb: ``` ##fileformat=VCFv4.1 ##INFO= ##INFO= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO NC_000012.11 88520131 23651 C ....
**Q1. Could you please clarify a recent change to the VCF file?** There was a recent (as far as I can tell) undocumented change to the VCF format - it...
On this page: https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/ There is a broken link to VCFs: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/ Should be https://ftp.ncbi.nih.gov/pub/clinvar/vcf_GRCh37/ https://ftp.ncbi.nih.gov/pub/clinvar/vcf_GRCh38/
If you have symbolic variants with the same chrom/pos/ref/alt but different SVLEN, they are treated as identical, meaning you silently drop symbolic variants Example VCF: ``` ##fileformat=VCFv4.1 ##INFO= ##INFO= #CHROM...
bcftools norm shifts symbolic <DEL> to position 1 without warning if the END tag is missing from VCF
Found while testing the changes in #1919 Leaving off the "END" tag causes `````` symbolic alts to shift to position 1 with no warning (DUP are fine). Sample output line:...
Hi, I discovered this while testing #2182 - it wasn't covered in the initial issue, so raising a new one Norm/remove dupes doesn't handle a VCF with 2 records that...
The current behavior of ```bcf_update_info``` in vcf.c is to use the END info tag to set rlen This field should instead be computed for symbolic variants (eg ``````) My interpretation...
https://asia.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000136250;r=7:36512941-36724494;t=ENST00000617537 Web page Reports that the sequence is 2385 bases long Ensembl API is in agreement: ``` In [25]: import requests In [26]: url = "https://rest.ensembl.org/sequence/id/ENST00000617537?type=cdna" In [27]: r =...