George F
UKB Community team
Data Analyst
Comments
Recent activity by George F
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Hi Baozhuo, Many UK Biobank BGEN fields are available as population VCFs (pVCF). To understand the duration could you provide some details about what are running (program, data-field, instance and ...
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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.pdfThis do...
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Hi Jonny,If you wish to filter the pVCF files, I would recommend submitting them as jobs, you can alter the instance and priority to reduce costs. bcftools and plink are part of the swiss-army-knif...
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We do not currently have a tutorial on how to do this but bcftools merge or plink are commonly used programs. The resulting file may to be very large so it filtering for relevant samples or regions...
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There is some documentation on how transform VCF to PLINK1.9 and BGEN (https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol/protocol-for-processing-ukb-who...
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I think the issue may be related to your java. I can compile successfully on both JupyterLab on RAP and through CLI on Ubuntu on my computer
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To get the cost of the jobs and other info use `dx describe job-######` the job cost is under “Total Price”. Replace the # with your job number.
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If you want to merge just the autosomes, don't include the relevant chromosomes in the files_to_merge.txt.I assume the command you're following is from 34:00 in the video.You can just edit the firs...
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I believe GCTA is available as a bash script. You could run it this way without downloading the plink files to your instance. https://yanglab.westlake.edu.cn/software/gcta/#Overview
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There are github notebooks which provide tutorials on how to filter the data (using python 101-103 and R 104-105) https://github.com/UK-Biobank/UKB-RAP-Notebooks/tree/main/NBs_Prelim
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