downloadable topmed dbsnp file for hg19

[raungar]

Hi-

Using your slivar tool has been wonderful and super helpful! I am wanting to annotate my VCFs in hg19 using TOPMed and gnomAD, but it seems the only linked hg19 files for annotations are for gnomAD. For TOPMed the only linked file for slivar is topmed.hg38.dbsnp.151.zip.

I imagine there are many people using your tool who would be interested in the hg19 version of this file, which is why I am posting an issue. I would find it really useful to have the file topmed.hg19.dbsnp.zip!

Thanks so much! Rachel

[brentp]

Hi Rachel, glad to hear the tool is useful! slivar has a command: slivar make-gnotate that will allow you to create your own gnotate file(s). You'll need the topmed/dbsnp vcf in hg19 of course but then it should be a single command to create your own zip (gnotate) file.

Happy to help if you have any troubles. I prefer to support the tool rather than try to add every possible zip file because users often want different columns, different builds, etc. and the number of possibilities is unmanageable. -B

[raungar]

That makes total sense! Thanks so much!

[raungar]

Hi-

I downloaded the topmed data, lifted over to hg19 using picard, and the used make-gnotate to make this file! I've attached this file in case it could be helpful to provide for others (though will delete from my drive after a week)

Thanks, Rachel topmed_hg19.zip https://drive.google.com/file/d/1DXG_b8oqO2_zDBhDespWkBk6x0wlyP_j/view?usp=drive_web

-Rachel

On Wed, Sep 22, 2021 at 3:00 AM Brent Pedersen @.***> wrote:

Hi Rachel, glad to hear the tool is useful! slivar has a command: slivar make-gnotate that will allow you to create your own gnotate file(s). You'll need the topmed/dbsnp vcf in hg19 of course but then it should be a single command to create your own zip (gnotate) file.

Happy to help if you have any troubles. I prefer to support the tool rather than try to add every possible zip file because users often want different columns, different builds, etc. and the number of possibilities is unmanageable. -B

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/slivar/issues/103#issuecomment-924774503, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEKVWXZEXN5IZZOQO7G4ZZTUDGSL5ANCNFSM5EPXGQLA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[brentp]

thanks Rachel, perhaps we could support this type of contribution by keeping a list of recipes (bash scripts or other) to make such zip files.

[raungar]

Sure! Step 1. Download topmed and hg19.fa and then liftover (topmed we already had, FA downloaded from here)

topmed_hg38="/path/freeze8.pass_only.phased.mesa_1319samples.maf01.biallelic.vcf.gz"
topmed_hg19="topmed_hg19.vcf.gz"
reject="REJECT_topmed_hg19.vcf.gz"
hg19_fa="/path/hg19.fa"
chain="hg38ToHg19.over.chain.gz"
picard LiftoverVcf I=$topmed_hg38 O=$topmed_hg19 CHAIN=$chain REJECT=$reject RECOVER_SWAPPED_REF_ALT=true R=$hg19_fa`

Step 2: run make-gnotate

               slivar make-gnotate \
                        --field AF:topmed_popmax_af \
                        --field AC:topmed_AC \
                        --prefix $my_prefix \
                        $topmed_hg19

[brentp]

thanks. I'll bookmark this and maybe create a collection of them.