Is it safe to remove VCF file after processing through seqr's pipeline?

[anjalijain22]

Hi Seqr Team,

Hope you're doing well!

We have a local installation of seqr and are annotating our datasets on prem. We're running out of storage space so I'm trying to find files that can be removed. I am wondering if it is safe to remove a VCF from the /mnt/data/seqr/data/input_vcfs/GRCh37 or /mnt/data/seqr/data/input_vcfs/GRCh38 directory after we have processed it through seqr's pipeline and just retain the .mt file in the directory? I tried it for one project and the variant search functionality seems to work just fine but just wanted to confirm with you in case there are some downstream consequences I may not be aware of?

Many thanks,
Anjali

[bpblanken]

Hi @anjalijain22!

For the purposes of variant search functionality, removing the VCF is just fine. However, we recommend you keep a copy of the raw VCF so you have it!

[bpblanken]

They .mt files produced by the pipeline may indeed be removed... the search functionality does not need them to work correctly.

[anjalijain22]

Amazing!!
I understand these are intermediate files, so is it okay to remove and not keep a back up or do you suggest I retain a copy of these elsewhere?

[anjalijain22]

Amazing!! I understand these are intermediate files, so is it okay to remove and not keep a back up or do you suggest I retain a copy of these elsewhere?

Hi @bpblanken, sorry to bother you again! Just wanted to follow up on my previous question regarding deletion of the .mt files. Really appreciate your help on this!

[bpblanken]

Yes, it is ok to not keep a back up! They are intermediate files that can be re-produced by running the pipeline over the same VCF.

[anjalijain22]

Perfect, thank you so much!!