I want to use WES data to perform analysis, but I can't find information on the exome sequencing batch. Second, are there principal components for WES data analysis?
I can only find the following description from Category 170.
?Exomes were captured with the IDT xGen Exome Research Panel v1.0 including supplemental probes. .... A different IDT v1.0 oligo lot was used in the initial 50k sequencing than was used in the sequencing of all subsequent samples. Inclusion of the is information as a covariate in downstream analyses is recommended.?
It's more than that, and the detail is already in category 170 doc that you shared above.
My personal recommendation is to focus on final released exome data which is already available and ignore all older releases unless you have already finished analyzing them. It's not just latest release, but it's final release, so this is the best time to jump into it.
Thank you for the reply. I found a paper (https://doi.org/10.1038/s41586-021-04103-z) that mentioned "for the analysis of exome data, we additionally included an indicator for exome sequencing batch (6 IDT batches) ", so I want to find the variable for batch.
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Here is the detailed documentation of WES
https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol
Thank you for replying! So, it means we could adjust the difference between the first 50k and the total 500k by excluding low read-depth variants?
It's more than that, and the detail is already in category 170 doc that you shared above.
My personal recommendation is to focus on final released exome data which is already available and ignore all older releases unless you have already finished analyzing them. It's not just latest release, but it's final release, so this is the best time to jump into it.
Thank you for the reply. I found a paper (https://doi.org/10.1038/s41586-021-04103-z) that mentioned "for the analysis of exome data, we additionally included an indicator for exome sequencing batch (6 IDT batches) ", so I want to find the variable for batch.
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