DReichLab/EIG

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Eigen tools by Nick Patterson and Alkes Price lab

Stars: 207
Forks: 61
Open beginner issues: 0
Indexed issues: 58

Dominant language: C
License: No license data
Last GitHub push: Jul 20, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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58 open issues indexed

Question Regarding SNP Count After Merging Genotype Files Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#114 · 1 comment · Opened Sep 29, 2025
Undefined behavior in PACKEDANCESTRYMAP hash code Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

DReichLab/EIG#113 · 1 comment · Opened Jun 19, 2025
How is estimated the genetic distance Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

DReichLab/EIG#112 · Opened Apr 22, 2025
smartpca: LAPACKE_dlange issue Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

DReichLab/EIG#110 · 1 comment · Opened Jan 21, 2025
Query about renaming first column of IND file Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

DReichLab/EIG#107 · 1 comment · Opened Sep 4, 2024
elliptical confidence not calculated Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

DReichLab/EIG#106 · 3 comments · Opened Jul 29, 2024
convertf exporting to PACKEDPED Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

DReichLab/EIG#105 · 1 comment · Opened Jun 18, 2024
numsnps output:0 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#104 · 1 comment · Opened May 19, 2024
FST details (by SNP FST) not printed Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

DReichLab/EIG#102 · 4 comments · Opened Apr 3, 2024
(getpedgenos) all.filter.ped bad geno * Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#101 · 1 comment · Opened Mar 14, 2024
Questions regarding multithreading Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

DReichLab/EIG#96 · Opened Oct 30, 2023
zz1 lines in logfile and run taking a very long time Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#95 · Opened Oct 25, 2023
obsolete finite function Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

DReichLab/EIG#92 · Opened Sep 18, 2023
XOR in snpsortit() of mcio.c Open

Difficulty 1/5 Under an hour Newbie friendliness 48/100

DReichLab/EIG#91 · Opened Aug 3, 2023
bad chrom: 100 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#88 · 2 comments · Opened May 17, 2023
Smartpca memory error Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

DReichLab/EIG#87 · 2 comments · Opened Apr 7, 2023
Issue when converting from plink to eigenstrat using convertf Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#86 · 4 comments · Opened Mar 7, 2023
.snp file format Open

Difficulty 2/5 1-3 hours Newbie friendliness 30/100

DReichLab/EIG#84 · 1 comment · Opened Jan 9, 2023
smartpca eigen vector file missing individuals Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#83 · 3 comments · Opened Nov 1, 2022
Error while working with Eigensoft command smartpca command Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

DReichLab/EIG#81 · 1 comment · Opened Sep 15, 2022
Unable to make bed *and* map for convertf Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

DReichLab/EIG#80 · 1 reaction · Opened Jul 19, 2022
Segmentation fault with 1000G but not with HM3 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#76 · 2 comments · Opened Mar 30, 2022
Error with smarteigenstrat.perl accepting pca output from smartpca.perl Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

DReichLab/EIG#75 · 4 comments · Opened Feb 18, 2022
(getpedgenos) bad geno <DEL> Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#74 · 1 comment · Opened Jan 4, 2022
Illegal instruction Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

DReichLab/EIG#72 · 4 comments · Opened Oct 18, 2021
maxpop 1000 Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

DReichLab/EIG#71 · 1 comment · Opened Oct 11, 2021
conda - smartpca stalling issue Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#70 · 5 comments · Opened Sep 2, 2021
Eigenstrat for 3 subpopulations Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

DReichLab/EIG#66 · 4 comments · Opened Jun 6, 2021
Unable to "make install" Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

DReichLab/EIG#65 · 1 comment · Opened Jun 4, 2021
Converted *.ancestrymapgeno still a binary file Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

DReichLab/EIG#61 · 5 comments · Opened Feb 26, 2021
Compiled programs no longer in bin Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

DReichLab/EIG#58 · 3 comments · Opened Dec 3, 2020
question about smarpca .perl -b parameter Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#51 · 3 comments · Opened Sep 10, 2020
Question: are there significant downsides to increasing IDSIZE? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#49 · Opened Aug 20, 2020
.snp error in Admixtools Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

DReichLab/EIG#47 · 2 comments · Opened May 13, 2020
sh: smartpca: command not found Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

DReichLab/EIG#46 · 6 comments · Opened Apr 24, 2020
Smartrel does not yield any output Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

DReichLab/EIG#44 · Opened Mar 31, 2020
Question about an error using smartpca Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

DReichLab/EIG#43 · 2 comments · Opened Feb 19, 2020
smartpca: columns of SNP weight matrix are not orthogonal with ldregress on Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#42 · 6 comments · Opened Feb 2, 2020
XTX has zero trace Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#41 · 5 comments · Opened Dec 17, 2019
population label characters cut off displayed in the log file Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

DReichLab/EIG#38 · Opened Sep 3, 2019
OOPS -i flag not specified at /usr/local/analysis/eigensoft/5.0.1/bin/smartpca.perl line 21. Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

DReichLab/EIG#35 · 3 comments · Opened Apr 25, 2019
.snp output format Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

DReichLab/EIG#33 · 8 comments · Opened Oct 2, 2018
smartpca output description Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#31 · 1 reaction · Opened Sep 5, 2018
shrinkage correction documentation Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#30 · 2 comments · Opened Jul 12, 2018
fsthiprecision still giving 3 decimal places Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#29 · 2 comments · Opened Jul 6, 2018
ksrc/kjg_gsl.c:10:21: fatal error: lapacke.h: No such file or directory Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

DReichLab/EIG#27 · 2 comments · Opened Jun 27, 2018
ID too long Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#26 · 5 comments · Opened May 28, 2018
Decimal places in EigenStrat p-values? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

DReichLab/EIG#24 · Opened Mar 1, 2018
please explain Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

DReichLab/EIG#23 · 5 comments · Opened Feb 7, 2018
pca selection statistic Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

DReichLab/EIG#21 · 2 comments · Opened Nov 22, 2017

DReichLab/EIG

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