Q: How to filter variants by a specific feature before --pick_order is applied?

[asalimih]

Hi, I'm using the --pick and --pick_order to customize the priority of transcript selection. Now for each variant I want to only consider transcripts which have a TSL number and then pick the one based on the priority I have specified in pick_order. I know there is a tsl option in pick_order but I guess it chooses the transcript with the lowest TSL number. my questions are:

• Is there any built-in solution for this?
• if not how should I approach it?
• Is there any other feature/option which is equivalent to having a TSL number?

Thanks in Advance

[nuno-agostinho]

Hi @asalimih,

Hope you are having a great day!

Just to make sure that I understand, you want to pick a specific transcript with a tsl other than the best available? So, for example, you want to pick a transcript of tsl=3 even if a tsl=1 exists?

Is there any other feature/option which is equivalent to having a TSL number?

We intend to provide an improved categorisation for transcript support that will supersede TSL in the future, but it's still in discussion.

You can look at other criteria used to prioritise transcripts, although they are not directly related with TSL, such as those described here.

Looking forward to your reply.

Cheers, Nuno

[asalimih]

Just to make sure that I understand, you want to pick a specific transcript with a tsl other than the best available? So, for example, you want to pick a transcript of tsl=3 even if a tsl=1 exists?

Hi @nuno-agostinho , Yes, and I want to choose the transcript with the highest impact (based on consequence) among those which have a tsl number (are not NA).

[nuno-agostinho]

Hi @asalimih,

I don't think there is a way to do that in VEP, but I think you can manually do something like:

• Do not use --pick, as it will return only one consequence per variant.
• Use --tsl to return the TSL number for each transcript.
• Use filter_vep to filter out consequences with no TSL number.
• From that result, you could create a custom script to go through each variant and select the consequence with highest impact based on your criteria.

Hope this helps.

Best, Nuno

[asalimih]

Thank you @nuno-agostinho, now I'm confident there isn't a simple built-in solution inside vep. It may be a useful feature if there was an option like --pre_filter with the filter_vep notation to filter transcripts before other options like --pick are applied.

[nuno-agostinho]

Hey @asalimih,

It may be a useful feature if there was an option like --pre_filter with the filter_vep notation to filter transcripts before other options like --pick are applied.

I will suggest a --pre_filter feature to our team for us to discuss it. Thank you!

I will now close this issue, but please feel free to open a new one if you encounter issues or have more suggestions on VEP.

Cheers, Nuno