Anastazie Sedlakova DNAnexus Team
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Recent activity by Anastazie Sedlakova
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Hello, here is general guidance , but please refer to your MTA. UKB RAP will restrict you to download WGS and WES data.https://dnanexus.gitbook.io/uk-biobank-rap/frequently-asked-questions#can-data...
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It depends on worker availability. By default, users are limited to 200 simultaneous workers at a time. For processing large sets of files, here is our guide to analyze large sample sets.
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I think that we are talking about two different things here. UKB-RAP has public rate card, available in from the documentation. UKB-RAP has only AWS instances, therefore, azure:mem3_ssd2_gpu4_x64 ...
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You can find link to it at UKB-RAP documentation.
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Can you please try to reproduce batch job using instructions for GUI or CLI?
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@Megan Ramaker? were you able to solve this issue? This might benefit to the whole community.
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One of the suggestions would be to use Swiss Army Knife(link requires log in to RAP) with vcftools, e.g.vcftools --gzvcf "$in_name" --positions "/mnt/project/example_list_of_positions.txt" --recode...
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What is the field ID that you want to download?
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You can use dx-toolkit, which is a set of command-line utilities to work with data on DNAnexus platform (UKB RAP). There are commands such as dx ls, dx cat, dx pwd etc. You do not need to run dx r...
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I did not find it explicitly in the regenie's documentation, but I m assuming that GENPOS is pulled from the set file (ukb23158_500k_OQFE.sets.txt.gz), where position in my opinion is defined by th...
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