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

jie huang, … Matthew Maher8

8:28 PM

plink2 --glm might be giving wrong result. please check this example out

Do you perhaps need an additional family="binomial" parameter on the R replication? This

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plink2 --glm might be giving wrong result. please check this example out

Do you perhaps need an additional family="binomial" parameter on the R replication? This

8:28 PM

Adam Willett, Christopher Chang4

12:12 PM

Single sample .bed and .bim file sizes

Sorry, that .log doesn't contain the error message, so I can't help you with that. Meanwhile,

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Single sample .bed and .bim file sizes

Sorry, that .log doesn't contain the error message, so I can't help you with that. Meanwhile,

12:12 PM

Sadikshya Sharma, … Amod Kumar7

1:53 AM

Plink1.9 solution

Thanks Amod! It helped. On Thu, May 9, 2024 at 8:57 PM Amod Kumar <amo...@gmail.com> wrote:

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Plink1.9 solution

Thanks Amod! It helped. On Thu, May 9, 2024 at 8:57 PM Amod Kumar <amo...@gmail.com> wrote:

1:53 AM

Sohom Dey, Christopher Chang2

May 9

rsID backfill error - Help

Please post a full .log file when asking for troubleshooting help.

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rsID backfill error - Help

Please post a full .log file when asking for troubleshooting help.

May 9

李志超, Christopher Chang2

May 9

categorical covar but doesnt work

Please post a full .log file when asking for troubleshooting help. On Thursday, May 9, 2024 at 9:15:

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categorical covar but doesnt work

Please post a full .log file when asking for troubleshooting help. On Thursday, May 9, 2024 at 9:15:

May 9

Efraín M, Christopher Chang4

May 7

How to exclude a variant by position

From the --set-missing-var-ids documentation on $1 and $2: "To maintain unique IDs in this

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How to exclude a variant by position

From the --set-missing-var-ids documentation on $1 and $2: "To maintain unique IDs in this

May 7

Dan Gealow, Christopher Chang4

May 6

Dosage rounding in --make-bed

The input is always a .pgen: https://www.cog-genomics.org/plink/2.0/input#keep_autoconv On Monday,

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Dosage rounding in --make-bed

The input is always a .pgen: https://www.cog-genomics.org/plink/2.0/input#keep_autoconv On Monday,

May 6

Matthew Maher, Christopher Chang3

May 5

seg-fault when using --r2-phased ref-based

thank you for the rapid fix! It runs without problem now when adding 'ref-based'. On Sunday,

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seg-fault when using --r2-phased ref-based

thank you for the rapid fix! It runs without problem now when adding 'ref-based'. On Sunday,

May 5

jie huang, Christopher Chang5

May 3

when allele freq is read in and wrote out in PLINK

Thanks. --glm produces per-phenotype output files, and all of its allele counts/frequencies are

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when allele freq is read in and wrote out in PLINK

Thanks. --glm produces per-phenotype output files, and all of its allele counts/frequencies are

May 3

Sue, Christopher Chang2

May 3

fewer tokens error

This error message suggests that there is a problem with the VCF file. Did you try to compare line

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fewer tokens error

This error message suggests that there is a problem with the VCF file. Did you try to compare line

May 3

Abhinandan S. Patil, Christopher Chang2

May 3

PLINK Epistasis analysis

No, it is necessary to start a separate PLINK 1.x run for each trait. On Wednesday, May 1, 2024 at 11

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PLINK Epistasis analysis

No, it is necessary to start a separate PLINK 1.x run for each trait. On Wednesday, May 1, 2024 at 11

May 3

Hye kyung Jeon, Christopher Chang2

May 3

plink - meta-anaylisis Error: No effect size field found in message error

Please post full .log file(s) when asking for troubleshooting help. On Wednesday, May 1, 2024 at 12:

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plink - meta-anaylisis Error: No effect size field found in message error

Please post full .log file(s) when asking for troubleshooting help. On Wednesday, May 1, 2024 at 12:

May 3

May 3

Removing 'chr' notation

Hello, I had previously added the chr with --update chr, for the correct notation for Michigan

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Removing 'chr' notation

Hello, I had previously added the chr with --update chr, for the correct notation for Michigan

May 3

Sjoerd Driessen, Christopher Chang5

May 2

INVALID_RESULT errcode

This fixed it, thanks! Op woensdag 1 mei 2024 om 15:50:59 UTC+2 schreef chrch...@gmail.com: There was

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INVALID_RESULT errcode

This fixed it, thanks! Op woensdag 1 mei 2024 om 15:50:59 UTC+2 schreef chrch...@gmail.com: There was

May 2

Nad, Christopher Chang2

May 1

SKAT reading encoding homozygous non-reference variants calls from plink as 0 instead of 2

This isn't plink-related. You need to check the documentation of the R package you're using,

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SKAT reading encoding homozygous non-reference variants calls from plink as 0 instead of 2

This isn't plink-related. You need to check the documentation of the R package you're using,

May 1

Samuel Hollinger, Christopher Chang2

May 1

treat chrX as autosome

You need to use --chr-set, not --allow-extra-chr, to specify a nonhuman chromosome set. Your command

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treat chrX as autosome

You need to use --chr-set, not --allow-extra-chr, to specify a nonhuman chromosome set. Your command

May 1

Sue, Matthew Maher5

Apr 30

GRS calculation and merging multiple bed files

I have encountered a challenge with the bim file I possess. The bim files are based on Axiom

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GRS calculation and merging multiple bed files

I have encountered a challenge with the bim file I possess. The bim files are based on Axiom

Apr 30

Nils Paffen, Christopher Chang19

Apr 29

Treating vcf-half-calls as "half-calls"

Alright. Thanks for your time and support. chrch...@gmail.com schrieb am Montag, 29. April 2024 um 20

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Treating vcf-half-calls as "half-calls"

Alright. Thanks for your time and support. chrch...@gmail.com schrieb am Montag, 29. April 2024 um 20

Apr 29

Kiran GL Lee, Christopher Chang3

Apr 29

Renaming chromosomes in ZW sex system

You are right. As it is a sex chromosome we might expect less variants anyway. Thank you. On Friday

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Renaming chromosomes in ZW sex system

You are right. As it is a sex chromosome we might expect less variants anyway. Thank you. On Friday

Apr 29

eran shaham, Christopher Chang3

Apr 26

For the record, this error was due to the original VCF input not actually being VCF. I will add a bit

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For the record, this error was due to the original VCF input not actually being VCF. I will add a bit

Apr 26

David Hamel Sellman, Chris Chang12

Apr 24

Determining reason for OBS_CT differing from expected sample size

I will plan on adding a warning, to be upgraded to an error requiring an explicit override in a

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Determining reason for OBS_CT differing from expected sample size

I will plan on adding a warning, to be upgraded to an error requiring an explicit override in a

Apr 24

Apr 24

--keep samples limit

--keep sample.list the sample_list have 2595 IDs,but the plink2 log shows 1391 samples (704 females,

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--keep samples limit

--keep sample.list the sample_list have 2595 IDs,but the plink2 log shows 1391 samples (704 females,

Apr 24

Tori Rudolph, Christopher Chang2

Apr 23

Creating .bed from .vcf

plink .bed files are "binary", not text. They aren't directly human-readable --

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Creating .bed from .vcf

plink .bed files are "binary", not text. They aren't directly human-readable --

Apr 23

kimberl...@gmail.com, Chris Chang2

Apr 23

Correct LD for covariates

Please provide or link to equations spelling out exactly what correction you have in mind. On Mon,

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Correct LD for covariates

Please provide or link to equations spelling out exactly what correction you have in mind. On Mon,

Apr 23

Yuri Morozov, Christopher Chang2

Apr 23

Reusing PLINK PCA for new samples

https://www.cog-genomics.org/plink/2.0/score#pca_project documents one way to approach this. On

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Reusing PLINK PCA for new samples

https://www.cog-genomics.org/plink/2.0/score#pca_project documents one way to approach this. On

Apr 23

Priyatam Dutta, Matthew Maher2

Apr 22

Filtering bgen based on UK Biobank sample

Filtering to only samples of interest should not cause loss of needed information. More importantly,

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Filtering bgen based on UK Biobank sample

Filtering to only samples of interest should not cause loss of needed information. More importantly,

Apr 22

Yiqi Zhao, Christopher Chang2

Apr 20

all_hg38.pgen.zst decompression failure

This is usually because the file wasn't fully downloaded. What is the size of the file? On Friday

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all_hg38.pgen.zst decompression failure

This is usually because the file wasn't fully downloaded. What is the size of the file? On Friday

Apr 20

Yorgos Bos, Christopher Chang5

Apr 19

Plink2 (development) --r2-unphased does not output snps in LD while they are there

This seems to fix our problem. Thanks for the quick fix! Op vrijdag 19 april 2024 om 08:12:47 UTC+2

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Plink2 (development) --r2-unphased does not output snps in LD while they are there

This seems to fix our problem. Thanks for the quick fix! Op vrijdag 19 april 2024 om 08:12:47 UTC+2

Apr 19

Matthew Maher, Christopher Chang2

Apr 19

Thanks. Bugfix is posted; let me know if you are still encountering a similar problem. On Thursday,

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Thanks. Bugfix is posted; let me know if you are still encountering a similar problem. On Thursday,

Apr 19

Bio Magician, Chris Chang2

Apr 18

Link in documention is broken

The PLINK/SEQ program referred to by that link is no longer maintained; I will remove the link. I

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Link in documention is broken

The PLINK/SEQ program referred to by that link is no longer maintained; I will remove the link. I

Apr 18

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