Issues

• Proposal: Minor Updates to Improve Tutorial Portability and Clarity

  MareesAT/GWA_tutorial#30 · Filter by author Truongphi20 opened on Nov 19, 2025

• Failed to unzip the genotype.vcf.gz in step 2: Population Stratification

  MareesAT/GWA_tutorial#26 · Filter by author giraffevzz opened on May 7, 2025
  2

• Failed to select autosomal SNPs only (QC Step 3)

  MareesAT/GWA_tutorial#25 · Filter by author Franklin593 opened on Jan 9, 2024

• Some questions about qqplots

  MareesAT/GWA_tutorial#24 · Filter by author Isa0529 opened on Sep 9, 2023

• why individual 13291 NA07045 in 0.2_low_call_rate_pihat.txt

  MareesAT/GWA_tutorial#23 · Filter by author usernicai opened on Aug 21, 2023
  1

• I have failed convert vcf to Plink(v1.07) format

  MareesAT/GWA_tutorial#20 · Filter by author Wusun5 opened on Sep 14, 2022
  1

• Failed to open snp_1_22.txt

  MareesAT/GWA_tutorial#19 · Filter by author TareqAldirawi opened on Jun 27, 2022

• Error: 'legend' is of length 0

  MareesAT/GWA_tutorial#18 · Filter by author Adonyo-Emmanuel opened on May 9, 2022
  3

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

  MareesAT/GWA_tutorial#17 · Filter by author SarojaSomu opened on Apr 13, 2022
  2

• Permutation step, Error? or My fault?

  MareesAT/GWA_tutorial#16 · Filter by author zzjl20 opened on Mar 15, 2022

• How to Create HapMap_3_r3 ( bim, bed and fam )

  MareesAT/GWA_tutorial#14 · Filter by author Kiran936 opened on Feb 11, 2022
  1

• data for 0.2_low_call_rate_pihat.txt

  MareesAT/GWA_tutorial#13 · Filter by author Manonanthini opened on Nov 18, 2021
  3

• Any plan to have an update to GWA_tutorial?

  MareesAT/GWA_tutorial#12 · Filter by author Shicheng-Guo opened on Oct 8, 2021
  1

• Quantitative phenotypes QC

  MareesAT/GWA_tutorial#11 · Filter by author elssam opened on Aug 7, 2021

• Miss MDS_merge2.mds file

  MareesAT/GWA_tutorial#10 · Filter by author Mohammad-Vahed opened on Mar 23, 2021
  1

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

  MareesAT/GWA_tutorial#9 · Filter by author 8865225 opened on Feb 16, 2021
  2

• How to confirm which sub has the lower call rate of each pair that I should remove

  MareesAT/GWA_tutorial#8 · Filter by author tongwang-en opened on Nov 26, 2020

• The system cannot find the path specified.

  MareesAT/GWA_tutorial#7 · Filter by author green-ear-rabbit opened on Aug 13, 2020

• .vcf has fewer tokens than expected error

  MareesAT/GWA_tutorial#5 · Filter by author sererenaa opened on Oct 18, 2019
  8

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

  MareesAT/GWA_tutorial#4 · Filter by author ulysses1881826 opened on Oct 12, 2019
  8

• p-value threshold for HWE deviation

  MareesAT/GWA_tutorial#3 · Filter by author blueskypie opened on Oct 2, 2018
  1

• controlling population stratification

  MareesAT/GWA_tutorial#2 · Filter by author blueskypie opened on Oct 2, 2018
  1

• convert vcf to plink step missing id setting

  MareesAT/GWA_tutorial#1 · Filter by author trptyrphe11 opened on Sep 7, 2018
  4