[ensembl-dev] VEP command line

[Linan, Margaret]

Thanks Irina,


Regarding the counting of the overlapped transcripts and regulatory features (using stats_html), should I just count how many times the string "transcript" or "regulatory features" appears in the 'Feature' column?

Also, what string would I be searching for in the 'Feature_type' column? In an example VEP annotated VCF, the only relevant string was: 'sense_overlapping'


Best regards,


Margaret Linan, MPH MS
Independent Consultant
Serving the CBIPM @ Icahn School of Medicine at Mount Sinai
Margaret.Linan at mssm.edu

________________________________
From: Irina Armean <iarmean at ebi.ac.uk>
Sent: Monday, September 16, 2019 8:22:53 AM
To: Ensembl developers list; Linan, Margaret
Subject: Re: [ensembl-dev] VEP command line

USE CAUTION: External Message.

Hi Margaret,


Sorry for the delay.

The stats written out in stats_html are collected internally simultaneously with the VEP annotation and therefore are not generated based on the VCF columns of the output file.


Depending on what VEP run options were selected, the counts could be reproduced based on the output file. For example the number of overlapped genes corresponds to the unique count of ENSG identifiers in the 'Gene' output column. The number of overlapped transcripts and regulatory features could be computed based on the 'Feature' and 'Feature_type' columns.



Kind regards,

Irina


On 12/09/2019 19:27, Linan, Margaret wrote:

Hi -


Does anyone know how the VEP command line program's stats_html utility calculates the following (i.e., what VCF columns and operations it uses)?

- VCF file pre-processing

- Number of overlapped genes

- Number of overlapped transcripts

- Number of overlapped regulatory features


Thank you,

Margaret



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