Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Switch parseVEP to using column names #542

Open
lydiayliu opened this issue Jul 27, 2022 · 0 comments
Open

Switch parseVEP to using column names #542

lydiayliu opened this issue Jul 27, 2022 · 0 comments
Labels
enhancement New feature or request

Comments

@lydiayliu
Copy link
Collaborator

#Uploaded_variation  Location    Allele  Gene                Feature             Feature_type  Consequence                         cDNA_position  CDS_position  Protein_position  Amino_acids  Codons   Existing_variation  Extra
1_12299290_C/A       1:12299290  A       ENSG00000048707.15  ENST00000011700.10  Transcript    stop_gained                         2590           2591          864               S/*          tCa/tAa  -                   IMPACT=HIGH;STRAND=1;SOURCE=GENCODEv34
1_12299290_C/A       1:12299290  A       ENSG00000048707     ENST00000011700     Transcript    stop_gained                         2590           2591          864               S/*          tCa/tAa  -                   IMPACT=HIGH;STRAND=1;FLAGS=cds_start_NF
1_12299290_C/A       1:12299290  A       ENSG00000048707.15  ENST00000460333.5   Transcript    non_coding_transcript_exon_variant  10             -             -                 -            -        -                   IMPACT=MODIFIER;STRAND=1;SOURCE=GENCODEv34
1_12299290_C/A       1:12299290  A       ENSG00000048707     ENST00000460333     Transcript    non_coding_transcript_exon_variant  10             -             -                 -            -        -                   IMPACT=MODIFIER;STRAND=1
1_12299290_C/A       1:12299290  A       ENSG00000048707.15  ENST00000613099.4   Transcript    stop_gained                         6252           6122          2041              S/*          tCa/tAa  -                   IMPACT=HIGH;STRAND=1;SOURCE=GENCODEv34

We currently just use "the first 13 columns"

@lydiayliu lydiayliu added the enhancement New feature or request label Jul 27, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

1 participant