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genome-in-a-bottle / giab_FAQ

This repository contains FAQs (Frequently Asked Questions) for genome in a bottle project
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GIAB Targeted data #1

Open jatintalwar opened 5 years ago

jatintalwar commented 5 years ago

Hello,

I see that most of the data resources provided for the GIAB samples are wither WGS or WES (similar). I was wondering if there is any source for targeted data (for eg: hybrid capture or amplicon based) at high depth (~500-100X)?

jzook commented 5 years ago

Although many clinical labs have likely generated targeted data like this, I don't know of any public data. We will keep this need in mind going forward. Would any targeted sequencing work for your needs, or do you need coverage of particular genes?

jatintalwar commented 5 years ago

Thank you for the reply..

I am not looking for a specific targeted sqeuencing data but a target that covers average size of around 1MB and covering at least 100-200 genes (with some intronic regions) would be good..

This is mostly useful for somatic panels as well..

jzook commented 5 years ago

The only current data I know about like this is for a sample from seracare that uses GIAB GM24385/HG002 as a background but has difficult clinical variants spiked into it. These data from Ion and Illumina targeted assays are here https://www.ncbi.nlm.nih.gov/bioproject/PRJNA526714

jatintalwar commented 5 years ago

Thank you very much for this resource. Might be useful for this application. But of course difficult to say if they are as comprehensive as a standard like GIAB. :)

Also different coverage levels might be a good variable to add to such a dataset.