plink2-users

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www.cog-genomics.org/plink/1.9/

www.cog-genomics.org/plink/2.0/

This is the primary technical support group for PLINK 1.9 and 2.0 users. Please post full .log file(s) when asking for troubleshooting help and/or reporting a bug.

It was previously also intended as a venue for other discussion of general interest to PLINK users, but there's too much technical-support traffic for that to work well. Instead:

- Major release announcements (including major bugfixes) are posted to the plink2-announce Google group. They will still be cross-posted to plink2-users.

- Feature requests and well-informed bug reports can be made at https://github.com/chrchang/plink-ng/issues . (But if you've encountered behavior where you're unsure whether it's a bug or a feature you're unaware of, plink2-users is better.) Feature requests can range from little bits of interface cleanup, to full calculations which cannot currently be performed at satisfactory speed/scale with existing software. Unexpected and unwanted incompatibilities between PLINK 1.9 and PLINK 1.07's interface count as bugs.

- Remarks on our documentation are welcome either here or on GitHub. We'll try to rewrite/redesign any parts that are confusing.

0 selected

Diego Salazar Tortosa

1:49 PM

Question about plink warnings

Hi Christopher, I am struggling a bit trying to understand some warnings of plink and the underlying

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Question about plink warnings

Hi Christopher, I am struggling a bit trying to understand some warnings of plink and the underlying

1:49 PM

MS WOO, Chris Chang11

Dec 11

UNFINISHED ERRCODE on logistic regression

First debug build has been posted to https://s3.amazonaws.com/plink2-assets/

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UNFINISHED ERRCODE on logistic regression

First debug build has been posted to https://s3.amazonaws.com/plink2-assets/

Dec 11

Georgii Dolgalev, Christopher Chang3

Dec 9

Use of MAP file with PLINK 1 dosages

With the new version from 6 December 2024, everything works. Thanks a lot for the quick help! суббота

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Use of MAP file with PLINK 1 dosages

With the new version from 6 December 2024, everything works. Thanks a lot for the quick help! суббота

Dec 9

Giulia Trauzzi, … DAVID J Cutler3

Dec 6

Plink2 --make-king

Guila, Just the dumbest question. In your command plink2 -pfile ../output/merged_filtered/

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Plink2 --make-king

Guila, Just the dumbest question. In your command plink2 -pfile ../output/merged_filtered/

Dec 6

SN, Chris Chang10

Dec 5

OBS_CT is lower than actual number of individuals

(or there are multiple variants with the same ID and their genotypes disagree) On Thu, Dec 5, 2024 at

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OBS_CT is lower than actual number of individuals

(or there are multiple variants with the same ID and their genotypes disagree) On Thu, Dec 5, 2024 at

Dec 5

bn, Christopher Chang3

Dec 4

filter whole chr

Great, thank you! On Tuesday, December 3, 2024 at 8:43:47 PM UTC-5 chrch...@gmail.com wrote: --not-

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filter whole chr

Great, thank you! On Tuesday, December 3, 2024 at 8:43:47 PM UTC-5 chrch...@gmail.com wrote: --not-

Dec 4

Dan Gealow, Christopher Chang3

Dec 3

plink2 alpha 6.2 segfault with --make-just-pvar cols=qual --sort-vars

Thanks for reporting this; bugfix is posted. On Monday, December 2, 2024 at 5:59:09 PM UTC-5 dge...@

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plink2 alpha 6.2 segfault with --make-just-pvar cols=qual --sort-vars

Thanks for reporting this; bugfix is posted. On Monday, December 2, 2024 at 5:59:09 PM UTC-5 dge...@

Dec 3

HA_63, Chris Chang3

Dec 3

Error: no samples in vcf file

The #CHROM header line is missing a sample-ID entry at the end, and this is why plink is complaining.

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Error: no samples in vcf file

The #CHROM header line is missing a sample-ID entry at the end, and this is why plink is complaining.

Dec 3

Dovini Jayasinghe, Christopher Chang3

Dec 1

How to enable performing GWAS using standardized genotypes in PLINK

thanks for confirming On Mon, 2 Dec 2024 at 1:46 AM, Christopher Chang <chrch...@gmail.com>

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How to enable performing GWAS using standardized genotypes in PLINK

thanks for confirming On Mon, 2 Dec 2024 at 1:46 AM, Christopher Chang <chrch...@gmail.com>

Dec 1

kaustubh...@gmail.com, Christopher Chang2

Dec 1

Behaviour of --const-fid in VCF import

From the --const-fid documentation: "A family ID ("FID") is optional. When it's

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Behaviour of --const-fid in VCF import

From the --const-fid documentation: "A family ID ("FID") is optional. When it's

Dec 1

Matthew Maher, Christopher Chang4

Dec 1

PLINK2 vcf import / sex info

Without sex information, allele frequency estimates are still good enough for --impute-sex's

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PLINK2 vcf import / sex info

Without sex information, allele frequency estimates are still good enough for --impute-sex's

Dec 1

Indrasen Chauhan

Dec 1

Scan complete, found 0 ROH

Dear Chris, I want to detect ROH in a goat breed using a 47-sample gvcf file. But I am not getting

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Scan complete, found 0 ROH

Dear Chris, I want to detect ROH in a goat breed using a 47-sample gvcf file. But I am not getting

Dec 1

Matthew Maher, Chris Chang4

Nov 29

New feature request (unless I'm unaware of existing)

I certainly understand the thought that pre-import filtering is out of scope for PLINK*, and may

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New feature request (unless I'm unaware of existing)

I certainly understand the thought that pre-import filtering is out of scope for PLINK*, and may

Nov 29

Giulia Pontali, Christopher Chang2

Nov 27

merge pgen-LD matrix

This error comes up when you have same-position, same-ID variants with dosage data: --pmerge-list

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merge pgen-LD matrix

This error comes up when you have same-position, same-ID variants with dosage data: --pmerge-list

Nov 27

BertHLV, Chris Chang5

Nov 27

Error Using king-cutoff: Failed to open king.id

As for plink 2.0 being more difficult to use than 1.x, this probably indicates a problem with the

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Error Using king-cutoff: Failed to open king.id

As for plink 2.0 being more difficult to use than 1.x, this probably indicates a problem with the

Nov 27

Matthew Maher, Chris Chang2

Nov 26

General Question on PLINK* file format

Related to (2), PLINK1 binary is simple enough that it's practical to write a reader from scratch

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General Question on PLINK* file format

Related to (2), PLINK1 binary is simple enough that it's practical to write a reader from scratch

Nov 26

kaustubh...@gmail.com, Christopher Chang3

Nov 25

Possible bug in Plink 2 --set-missing-var-ids

Great, thank you! On Sunday, 24 November 2024 at 16:45:42 UTC chrch...@gmail.com wrote: Thanks for

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Possible bug in Plink 2 --set-missing-var-ids

Great, thank you! On Sunday, 24 November 2024 at 16:45:42 UTC chrch...@gmail.com wrote: Thanks for

Nov 25

nag...@oregonstate.edu, … Christopher Chang4

Nov 24

PLINK 1.9: When lowering missing rate filter (`geno`), more SNPs retained

The log indicates that there are no missing genotypes in the dataset. (Incidentally, there was a

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PLINK 1.9: When lowering missing rate filter (`geno`), more SNPs retained

The log indicates that there are no missing genotypes in the dataset. (Incidentally, there was a

Nov 24

Melissa Naugle, … Abdirahman Ali4

Nov 21

--ld-window clarification

Hi Adonyo, There is no correct answer(s) to your questions as it is dependent on your aims, purpose

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--ld-window clarification

Hi Adonyo, There is no correct answer(s) to your questions as it is dependent on your aims, purpose

Nov 21

Soumeen Jin, Christopher Chang2

Nov 17

error in --update-chr in plink2

I've added the following note to the bottom of the --update-chr documentation: "Also note

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error in --update-chr in plink2

I've added the following note to the bottom of the --update-chr documentation: "Also note

Nov 17

Nov 16

Hi there, has somebody expereince with roh analysis in plink via Gorssen R skript? Thanks

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Hi there, has somebody expereince with roh analysis in plink via Gorssen R skript? Thanks

Nov 16

Zhixiu Li, Christopher Chang4

Nov 15

UNFINISHED PLINK2 regression

Thanks. From the --glm documentation: "Finally, the statistics computed by --glm are not

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UNFINISHED PLINK2 regression

Thanks. From the --glm documentation: "Finally, the statistics computed by --glm are not

Nov 15

Lucas Fishbein, … Christopher Chang5

Nov 14

Plink2 Segmentation fault upon --make-pgen when --removing or --keep flag is utalized

Thanks. Bugfix is posted; let me know if you still see any problems. On Thursday, November 14, 2024

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Plink2 Segmentation fault upon --make-pgen when --removing or --keep flag is utalized

Thanks. Bugfix is posted; let me know if you still see any problems. On Thursday, November 14, 2024

Nov 14

SN, Christopher Chang2

Nov 14

converting plink files from rsIDs to chr:pos:a1:a2 format

Simplest method is with plink 2.0's --set-all-var-ids flag.

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converting plink files from rsIDs to chr:pos:a1:a2 format

Simplest method is with plink 2.0's --set-all-var-ids flag.

Nov 14

Kuoshng Hung, Christopher Chang3

Nov 14

What is user_1DF mrans in --tests?

Oops, I somehow missed the "3" in your parameters when writing the previous response. The

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What is user_1DF mrans in --tests?

Oops, I somehow missed the "3" in your parameters when writing the previous response. The

Nov 14

Hasuni, Chris Chang3

Nov 13

--score file entries were skipped due to mismatching allele codes

See the current PCA projection documentation ( https://www.cog-genomics.org/plink/2.0/score#

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--score file entries were skipped due to mismatching allele codes

See the current PCA projection documentation ( https://www.cog-genomics.org/plink/2.0/score#

Nov 13

yujin kim, … DAVID J Cutler5

Nov 13

[Logistic Regression ERROR]

Dear Dave, I've finally realized what the issue was. Thanks to you, I've learned a lot. In

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[Logistic Regression ERROR]

Dear Dave, I've finally realized what the issue was. Thanks to you, I've learned a lot. In

Nov 13

Aish, Chris Chang4

Nov 11

Clarification for why there is varying OBS_CT

That explains it so well; thank you so much! Thanks again, Aish On Monday, November 11, 2024 at 7:10:

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Clarification for why there is varying OBS_CT

That explains it so well; thank you so much! Thanks again, Aish On Monday, November 11, 2024 at 7:10:

Nov 11

Nov 8

.bim .bed .fam Formate conversion to VCF file

Hi I am working with PPMI dataset and I have .bim, .bed and .fam files. I am Computer science student

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.bim .bed .fam Formate conversion to VCF file

Hi I am working with PPMI dataset and I have .bim, .bed and .fam files. I am Computer science student

Nov 8

Nov 6

PRS --score DENOM as ALLELE_CT

Hello Chris and the PLINK community, I am constructing a PRS using clumping and thresholding. There

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PRS --score DENOM as ALLELE_CT

Hello Chris and the PLINK community, I am constructing a PRS using clumping and thresholding. There

Nov 6

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