In the DNAnexsus user guide the cohort browser has two tabs, one for phenotypic information and another for genomic. My project has access to both but on the cohort browser I am only able to access the phenotypes. I can see the exome sequencing as entries but am unable to subset by genomic region, rarity etc.
I am trying to pull out a phenotype and then subset it by those with and without rare, damaging variants (as per gnomAD and CADD) in a particular set of genomic regions.
Many thanks
Hi folks! Inre subsetting exomes by genomic region I am giving a webinar with regeneron and nvidia on 2/17 and will touch on how to do that.
If you have the original, non-exome genotype data, its quite easy to subset using the cohort browser.
That said, if you want to subset with annotations, I believe gnomAD and ClinVar are available for your use in UKBRAP.
Personally (my opinion, not DNAnexus'), I use opencravat (opencravat.org) for these types of things. Its really easy to implement in a jupyter notebook.
Some of the exome data is on the genome browser, if yours is not, if it were me, I would use bedtools. I show how to use bedtools on the UKBRAP toward the end of this webinar (theres a link to view on demand if you scroll down):
Actually, while thats a good start, it goes much deeper than that. Thats something I'll plan to cover in our UKBRAP workshop coming up in a couple of weeks (the announcement should be out early next week!)
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just saying that this is exactly what I am trying to do and need guidance...
Hi folks! Inre subsetting exomes by genomic region I am giving a webinar with regeneron and nvidia on 2/17 and will touch on how to do that.
If you have the original, non-exome genotype data, its quite easy to subset using the cohort browser.
That said, if you want to subset with annotations, I believe gnomAD and ClinVar are available for your use in UKBRAP.
Personally (my opinion, not DNAnexus'), I use opencravat (opencravat.org) for these types of things. Its really easy to implement in a jupyter notebook.
and if you want to know how to use a Jupyter notebook on UKBRAP, check this out: https://www.youtube.com/watch?v=YIPdhf3qbQA !
@Ben Busby? Great webinar today but it did not mention how to subset samples by genotype. Is there another webinar for this?
Or if there could be page added to the (very useful!) DNAnexsus guide......
Dear @Ben Busby? ,
I was wondering if anyone could help with this issue?
Many thanks
Some of the exome data is on the genome browser, if yours is not, if it were me, I would use bedtools. I show how to use bedtools on the UKBRAP toward the end of this webinar (theres a link to view on demand if you scroll down):
https://community.dnanexus.com/s/question/0D5t000003l93UECAY/webinar-feb-24-visualizing-and-annotating-gwas-results-on-the-uk-biobank-research-analysis-platform
Actually, while thats a good start, it goes much deeper than that. Thats something I'll plan to cover in our UKBRAP workshop coming up in a couple of weeks (the announcement should be out early next week!)
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