Former User of DNAx Community_28
Comments
Recent activity by Former User of DNAx Community_28
-
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...
- View comment
- 0 votes
-
{@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...
- View comment
- 0 votes
-
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...
- View comment
- 0 votes
-
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...
- View comment
- 0 votes
-
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...
- View comment
- 0 votes
-
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...
- View comment
- 0 votes
-
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 ...
- View comment
- 0 votes
-
If you are using dx tools on a linux or mac via the command line, you can create a files_to_merge.txt file by running these commands on your local computer: dx ls Bulk/Whole\ genome\ sequences/Who...
- View comment
- 0 votes
-
@Vignesh Arunachalam? , First I wrote and published a script to create the list of all the WGS pVCF segments per chromosome here: https://github.com/pjgreer/ukb-rap-tools/blob/main/ukb-vcf-list.sh ...
- View comment
- 0 votes
-
I am not sure what type of regeneie analysis you are running, but I wrote a GWAS tutorial a few months ago and the last step of the tutorial is to combine all the association files from each chromo...
- View comment
- 0 votes