Anastazie Sedlakova DNAnexus Team
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Recent activity by Anastazie Sedlakova
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I can reproduce your problem. It is probably caused by presence of missing values for some samples. What solved the issue for me is ignoring phenotypes using --no-fam-pheno parameter, e.g.: plink2 ...
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In cohort browser, you can use Variant browser. Population Allele Frequency there is computed using 450k WES data
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Yes, you will see GENO tab only if you have access to 450K WES data. In other case it is better to proceed with PLINK2, it is installed in Swiss Army Knife tool (you need to log into RAP to open th...
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Hello, that is strange, link that I provided worked for me. Nevertheless it is fine that samtools are much faster now. Is FASTA file that you used GRCh38.primary_assembly.genome.fa?
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Hello,when we work with CRAM files we usually provide reference file using -T parameter, see example here. You can download reference file here or here is described how you can figure out the refer...
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Hello, on our GWAS visualization webinar we were showing how you can preprocess regenie output, so that all results are in one file. Here is example code that you can use: # Concatenate files, assu...
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Can you please check the data field ID? Here is the list of WGS/WES fields currently available on UKB RAP.
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This data field is currently restricted and is not available on UKB RAP. This particular field is planned to be released later this year, probably in November. In case you want to know more inform...
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Hello, here is the Jupyter notebook which is extracting 41270 field - Summary ICD10 diagnosis. Here is my proposed workflow to extract lets say thyroid cancer (ICD10 C73 code): Extract 41270 field ...
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If the data is in PLINK or BGEN format you can use PLINK2 to extract samples by using --keep parameter .For example, if you are using final exome release (field ID 23158) plink2 --bfile ukb23158_c2...
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