GWA_tutorial

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Hi, I am running the codes and I got an error in the following code: ### Step 3 ### # Generate bfile with autosomal SNPs only and delete SNPs with...

TareqAldirawi

Error: 'legend' is of length 0

3

When generating a plot to assess the type of relationship in the sample, I do get an R script erro. $ Rscript --no-save Relatedness.R Error in legend(1, 1, xjust =...

Adonyo-Emmanuel

ftp vs https in downloading 1000 genome vcf file in Step 2_Population_stratification

2

Hi, I noticed using the command wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz from the 2_Main_script_MDS.txt downloads a corrupted file. Hence creating plink files from the vcf resulted in file read failure error. But when...

SarojaSomu

I am reproducing the whole tutorial. At , ##Permutation: The reduce computational time we only perform this test on a subset of the SNPs from chromosome 22. `awk '{ if...

zzjl20

data for 0.2_low_call_rate_pihat.txt

3

Hi Marees, Thanks for the pipeline. I have around 5k samples in pihat_min0.2_genome and 390 in zoom_pihat_genome. If I sort them, I could identify the related individuals but don't know...

Manonanthini

Can you explain more about the "inversion.txt" in the 1_QC_GWAS folder

8

Thank you for your tutorial in advance. I have some confusion about the "inversion.txt" in the 1_QC_GWAS folder. I know it is for excluding high inversion regions. However, where is...

ulysses1881826

.vcf has fewer tokens than expected error

8

In part 2, when we convert from vcf to Plink format, I get an error:  Any advice to get around this? I end up with temporary files because of...

sererenaa

How to Create HapMap_3_r3 ( bim, bed and fam )

1

Hi, I am new to GWAS, I have 100+ exome SNV annotated files, i want to create same bim, bed and fam files. Can you/anyone pls help me with how...

Kiran936

Could you please tell me how to "inversion.txt" in the 1_QC_GWAS folder

2

I want to practice my genetic data following your tutorial, but I do not know how to create the mydata-based inversion.txt file. Could you please tell me in detail. Thank...

8865225

Any plan to have an update to GWA_tutorial?

1

Hi Andries, any plan to have an update to GWA_tutorial? Shicheng

Shicheng-Guo