George F
UKB Community team
Data Analyst
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Recent activity by George F
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There are pVCFs (population VCFs) available for all 500K participants (see https://biobank.ctsu.ox.ac.uk/showcase/label.cgi?id=180). Common filtering tools (bcftools, plink) are available as part o...
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If you wish to combine SNP (such as genotype) with phenotypic information, the pVCFs may be useful. You can generate a list of participants that you are interested based on their phenotypic informa...
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Hi Mitja,The 500K GATK/Graphtyper and DRAGEN datasets are currently only available in pVCF format. We are currently working to release as PLINK and BGEN.The 200K version of the GATK/Graphtyper data...
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A GLnexus manifest file has one gVCF filename per line. (https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started)Example code f how to make one can be found here:https://dnanexus.gitbook.io/uk...
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It is possible to convert the pVCFs to BGEN and PLINK. There is a protocol here: https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol/protocol-for-processi...
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I think it would be more efficient if you parallelised your swiss-army-knife iewhile read f; do \ dx run swiss-army-knife \ -iin="${project}/script.sh" \ -icmd="bash script.sh '$i'" \ --instance-ty...
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To answer the second part of your question, the “b”-numbering pVCFs, list all the variants within a chunk of chromosome co-ordinates (approx 20000 bp per chunk for field 24310). Note that areas of...
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Hi,To date we have not had queries from other researchers regarding this filtering file (the last update was in July 2022).For more information about how this file was generated please see: https:/...
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You can extract a snp or a list of snps using the --extract option on plink ie:grep Affx-3446195 ukb22418_cMT_b0_v2.bim > extract_SNPs.txtplink --bfile ukb22418_cMT_b0_v2 --extract extract_SNPs.txt...
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Yes, withdrawn participants will be removed from all data following a refresh.
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