Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Hello, as far as I know, the dxfuse, i.e. "/mnt/project/" is not available/preinstalled everywhere. It is part of Swiss Army Knife, JupyterLab and also ttyd, but for instance not available in apple...
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I would check Bulk/Imputation/UKB imputation from genotype in terms of which field id you work with. Later, I would go to https://biobank.ndph.ox.ac.uk/showcase/search.cgi and search relevant field...
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This kind of error might be caused by out-of-memory error. Consider using a more powerful instance for the job. If this persists, I would send it to ukbiobank-support@dnanexus.com for a detailed in...
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I have not used the specific tools mentioned your questions but I am responding to give you tips around tool building. You will be able to bring your own tools on the UKB-RAP. If the tools have the...
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Hi @Katreya Lovrenert?, is this helping you to resolve this? https://dnanexus.gitbook.io/uk-biobank-rap/frequently-asked-questions#are-the-headers-of-gvcf-or-cram-files-pseudonymized
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Yes, I would say so. Sounds good. Try to use it as input file for your Swiss Army Knife job.
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The error message "[E::idx_find_and_load] Could not retrieve index file for '1798762.snpEff.vcf.gz'" indicates that for running bcftools, you will need to provide an index file for your vcf file. U...
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Hi @Burcu Çevik?, What I would do - I would run JupyterLab and explore the vcf there.If you prefer bash, one good option is to use vcftools [https://vcftools.sourceforge.net/man_latest.html].If yo...
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Here is recently shared info about Olink data: https://community.dnanexus.com/s/question/0D582000000jnRACAY/new-data-release-on-ukbrap-olink-proteomics-data Data documentation is then available her...
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I am wondering whether there would an alternative way of doing this, e.g. load and read PLINK (bed, bim, fam) or BGEN rather than pVCF. PLINK or BGEN are available per chromosome.
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