some questions about the Whole exome sequencing analysis(variants filtering)
When performing variants quality control,I notice the pVCF offered by UKB does't treat with filtering. Now, I have set a filter standards, but I wonder which tool I should choose to perform data filtering and how to perform HWE test.
Besides, does the genotype in pVCF has treated with quality control?
thank you very much!
Comments
1 comment
Hi Yaying,
The WES FAQ page contains information about several aspects of the WES pVCFs. https://www.ukbiobank.ac.uk/media/najcnoaz/access_064-uk-biobank-exome-release-faq_v11-1_final-002.pdf
This document provides links to filtering examples, including WES Analysis Best Practices ( https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=914 ) which recommends filtering for read depth using plink.
The FAQ document also states “To ensure that the final exome release data support a broad range of analyses, no variant- or sample-level filters were pre-applied to the pVCF or PLINK files.”
Thank you for getting in touch, we hope this has been helpful.
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