Former User of DNAx Community_28
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Recent activity by Former User of DNAx Community_28
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You should search the forum for prior posts on the topic. or check the dnanexus gitbook. (linked below) I have a github with code for running both rare variant as well as gwas using dx run cli. If ...
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The dx submission scripts can be looped over the files you are running them upon. (ie. each chromosome file, or each individual). If you look at the swiss -army-knife log file, you will see that e...
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1) you likely only need to run this on, at most, 12 chromosomes. (12 snps, 1 snp per chromosome) 2) Since you are converting the vcf file to plink in the last stage, You should consider using p...
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I never bothered with different thresholds for cases and controls because when you reject a SNP in either, it will not be included in the analysis. I always used the case threshold cutoff for the p...
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{@005t0000009gPQNAA2}? If you are running swiss-army-knife via a dx run shell script like in the dnanexus gwas github repositories, you can simply add the install lines into your execution script...
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The easiest way to use UKB field 22021. "Genetic kinship to other participants" get the list of all eids where f22021==0. That will give you a total of 339516 subjects who are completely unrelated...
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Just a heads up. While the instructions state clearly that you need to run liftover from grch37 to grch38 on the array data on page 45 of the slide deck. The merge command is clearly using the grch...
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Nihal, Saige, plink, and regenie all require similar QC steps prior to GWAS. Depending on the datasource: base-GT, Imputed-GT, or WES, You will have very slightly different QC parameters. I have a...
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Removing highly related individuals and sex mismatch can be done when building the phenotype file. There is a tutorial using python here, but I prefer using R.https://dnanexus.gitbook.io/uk-bioban...
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There are many tools, but this is a multi-step process. Each chromosome has many segments in its pvcf file. you need to filter and concatenate across all of the segments for each chromosome. There ...
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