Anastazie Sedlakova DNAnexus Team
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Recent activity by Anastazie Sedlakova
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As fas as I know, there is overall heterozygosity and ancestry corrected. If you want to calculate X chromosome heterozygosity I suggest following approach using array data , however, I did not tri...
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I am not sure what exact command you were using. When looking at the Cohort Browser, field 20002 has multiple instances, see printscreen. If using dx extract_dataset, you should specify each instan...
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I do not know what is the exact command that you are running. If you are trying something along the lines of creating a file, then appending to it with another process that won't work, it needs to ...
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Community members do not have access to DNAnexus' support system. Can you please share relevant details from your communication with the support team? It is more efficient to use only one channel t...
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Can you please post the specific errors that you are getting? From the EIGENSOFT FAQ page it looks like memory is the main limiting factor when scaling up the sample size. What instance did you try...
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Are you running EIGENSOFT on array or WES data?
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@Ondrej Klempir? so when using dx extract_dataset i need to use field titles as entity name + field name?e.g. $cat query_of_the_week_1.data_dictionary.csv | grep "participant" | grep "Age at recrui...
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Both sample level gVCFs and a joint-genotyped set (PLINK, BGEN and pVCF) are unfiltered to maximize a broad range of analyses and researchers will need to carefully consider an appropriate filterin...
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Here is more information about VCF filtering, e.g. DP>=10 filtering. The protocol linked applies to WES 300k, 450k, and the final release.
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Did you install dxCompiler on your computer? It has to be on your computer, not in the UKB RAP project folder.
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