plink2-dev

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This is for discussion of the plink-ng source code and its documentation, including build issues.

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jane Chang, Christopher Chang2

Mar 21

https://www.cog-genomics.org/plink/2.0/general_usage On Thursday, March 21, 2024 at 6:43:54 PM UTC-7

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https://www.cog-genomics.org/plink/2.0/general_usage On Thursday, March 21, 2024 at 6:43:54 PM UTC-7

Mar 21

Chris Norman, Christopher Chang4

11/6/23

Handling partially phased variant sites correctly in pgenlib

Ok, it looks like what I was seeing was a failure because I was making an incorrect assumption about

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Handling partially phased variant sites correctly in pgenlib

Ok, it looks like what I was seeing was a failure because I was making an incorrect assumption about

11/6/23

Chris Norman, Christopher Chang8

9/15/23

How to present non-autosomal haploid genotypes to plink2 PGEN API

Oh ok, interesting - I would have thought that the .pvar and .pgen would have to be kept in sync for

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How to present non-autosomal haploid genotypes to plink2 PGEN API

Oh ok, interesting - I would have thought that the .pvar and .pgen would have to be kept in sync for

9/15/23

Yeajin Song, Christopher Chang2

6/12/23

Read pgen files

1. Have you tried "pip install pgenlib" (or "pip3 install pgenlib")? 2. No; from

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Read pgen files

1. Have you tried "pip install pgenlib" (or "pip3 install pgenlib")? 2. No; from

6/12/23

Chris Norman, Christopher Chang4

6/6/23

Writing a pgen without knowing the number of variants of front

Ok, thanks for the quick response. So I'll always use plink2::kPglMaxVariantCt as my variant

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Writing a pgen without knowing the number of variants of front

Ok, thanks for the quick response. So I'll always use plink2::kPglMaxVariantCt as my variant

6/6/23

Tejas D Hasarali, Christopher Chang5

4/28/23

Having compilation issues in aarch64 architecture with 1.90

Thank you for the quick response, I used the git repo and I was able to build the the executable in

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Having compilation issues in aarch64 architecture with 1.90

Thank you for the quick response, I used the git repo and I was able to build the the executable in

4/28/23

2/6/23

model-genotypic

Hi, I have a question about calculate polygenic risk score when the association test is 2-df(model

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model-genotypic

Hi, I have a question about calculate polygenic risk score when the association test is 2-df(model

2/6/23

Sandeep Pulla, Christopher Chang3

1/12/23

BED file format genotype code change?

Thank you for the clarification. PLINK 1.9 documentation is indeed clearer in this regard. Thanks,

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BED file format genotype code change?

Thank you for the clarification. PLINK 1.9 documentation is indeed clearer in this regard. Thanks,

1/12/23

choish...@gmail.com, Christopher Chang3

10/25/22

Expected behaviour regarding malformed psam files

Perfect, thank you! On Monday, 24 October 2022 at 14:45:35 UTC-4 chrch...@gmail.com wrote: ".fam

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Expected behaviour regarding malformed psam files

Perfect, thank you! On Monday, 24 October 2022 at 14:45:35 UTC-4 chrch...@gmail.com wrote: ".fam

10/25/22

choish...@gmail.com, Christopher Chang3

3/10/22

Additional allele_ct_bases in score report for haploid

Bugfix is posted. On Thursday, March 10, 2022 at 8:01:24 AM UTC-8 choish...@gmail.com wrote: Hi Chris

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Additional allele_ct_bases in score report for haploid

Bugfix is posted. On Thursday, March 10, 2022 at 8:01:24 AM UTC-8 choish...@gmail.com wrote: Hi Chris

3/10/22

choish...@gmail.com, Christopher Chang3

2/24/22

Assert fail for LD

That's really quick! Thanks so much! On Thursday, 24 February 2022 at 00:56:28 UTC-5 chrch...@

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Assert fail for LD

That's really quick! Thanks so much! On Thursday, 24 February 2022 at 00:56:28 UTC-5 chrch...@

2/24/22

choish...@gmail.com, Christopher Chang14

2/21/22

Pgfi initiation

Thank you so much! That should solve all my problem for now Sam On Monday, 21 February 2022 at 13:18:

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Pgfi initiation

Thank you so much! That should solve all my problem for now Sam On Monday, 21 February 2022 at 13:18:

2/21/22

choish...@gmail.com, Christopher Chang9

1/5/22

plink2_text library

That's exactly what I needed. Thanks Chris! On Wednesday, 5 January 2022 at 17:57:25 UTC-5 chrch.

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plink2_text library

That's exactly what I needed. Thanks Chris! On Wednesday, 5 January 2022 at 17:57:25 UTC-5 chrch.

1/5/22

Joelle Mbatchou, Christopher Chang5

4/12/21

C++ pen library

Ah okay, that makes more sense. Will try again with these modification. Thank you! On Monday, April

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C++ pen library

Ah okay, that makes more sense. Will try again with these modification. Thank you! On Monday, April

4/12/21

Thon de Boer, Christopher Chang2

3/15/21

Getting truncated PVAR file when converting BGEN file

For the record, this was resolved in plink2-users: https://groups.google.com/g/plink2-users/c/

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Getting truncated PVAR file when converting BGEN file

For the record, this was resolved in plink2-users: https://groups.google.com/g/plink2-users/c/

3/15/21

N., Christopher Chang5

1/25/21

pgenlibr: what is the fastest way to get the index of a variant by variant-ID?

Awesome, thank you. On Monday, January 25, 2021 at 3:08:27 AM UTC+1 chrch...@gmail.com wrote: I'

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pgenlibr: what is the fastest way to get the index of a variant by variant-ID?

Awesome, thank you. On Monday, January 25, 2021 at 3:08:27 AM UTC+1 chrch...@gmail.com wrote: I'

1/25/21

AR, Christopher Chang5

10/21/19

--score : Single sample v/s multisample output difference in plink 1.9

That's because you created a .bim file lacking most of the alleles. If you start with the .ped

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--score : Single sample v/s multisample output difference in plink 1.9

That's because you created a .bim file lacking most of the alleles. If you start with the .ped

10/21/19

Akash Ramachandran, Christopher Chang3

10/18/19

clang: error: no such file or directory: '../zlib-1.2.11/libz.so.1.2.11'

Thanks! That was helpful. On Thursday, October 17, 2019 at 7:23:34 PM UTC-7, Christopher Chang wrote:

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clang: error: no such file or directory: '../zlib-1.2.11/libz.so.1.2.11'

Thanks! That was helpful. On Thursday, October 17, 2019 at 7:23:34 PM UTC-7, Christopher Chang wrote:

10/18/19

Akhil Pampana, Christopher Chang2

10/7/19

phased data for plink2 alpha

This type of question is more appropriate for the plink2-users group. But yes, plink2 shouldn't

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phased data for plink2 alpha

This type of question is more appropriate for the plink2-users group. But yes, plink2 shouldn't

10/7/19

preetilak...@gmail.com, Christopher Chang2

6/16/19

hapmap3 data in PLINK format

Sorry about neglecting this post for so long. While there are no plans to add this to the official

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hapmap3 data in PLINK format

Sorry about neglecting this post for so long. While there are no plans to add this to the official

6/16/19

Paolo Di Domenico, Christopher Chang2

6/16/19

Merge multicore

Hi Paolo, The plink2 merger will definitely use more than 1 thread, but it also has to deal with a

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Merge multicore

Hi Paolo, The plink2 merger will definitely use more than 1 thread, but it also has to deal with a

6/16/19

Alexis Dereeper, … Lance Parsons4

10/26/17

plink in Galaxy

Galaxy supports using conda packages for dependencies such as PLINK. I'd highly recommend using

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plink in Galaxy

Galaxy supports using conda packages for dependencies such as PLINK. I'd highly recommend using

10/26/17

Shing Wan Choi, Christopher Chang2

2/23/17

Stack Smashing Detected

Yes, this analysis looks correct to me; thanks for reporting it! I will post a build with this change

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Stack Smashing Detected

Yes, this analysis looks correct to me; thanks for reporting it! I will post a build with this change

2/23/17

Mike Jarsulic, Christopher Chang2

2/17/17

Unable to link to Atlas

Possibly relevant: http://stackoverflow.com/questions/31038366/atlas-lapack-not-linking-to-blas On

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Unable to link to Atlas

Possibly relevant: http://stackoverflow.com/questions/31038366/atlas-lapack-not-linking-to-blas On

2/17/17

Julio Rodríguez

10/5/16

Problems Filtering of CNV data based on frequency

Hi, there is a problem with the alternative frequency filtering approach. The --cnv-freq-exclude-

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Problems Filtering of CNV data based on frequency

Hi, there is a problem with the alternative frequency filtering approach. The --cnv-freq-exclude-

10/5/16

Raymond Walters, Christopher Chang4

4/19/16

R plugin problems

Hi Chris, Unfortunately those logs got overwritten by re-runs to work around this issue in the past

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R plugin problems

Hi Chris, Unfortunately those logs got overwritten by re-runs to work around this issue in the past

4/19/16

Stéphanie Arnoux, Christopher Chang3

3/1/16

Segmentation fault: 11 with allow(ED)-extra-chr data.

Hi, I just downloaded the 24th Feb version and it solved the --indep-pairwise error.r But I still

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Segmentation fault: 11 with allow(ED)-extra-chr data.

Hi, I just downloaded the 24th Feb version and it solved the --indep-pairwise error.r But I still

3/1/16

William Gilks, Christopher Chang2

7/17/15

writing code for haploid QT assoc

What other programming languages are you familiar with? I ask because, (i) if you have *no* previous

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writing code for haploid QT assoc

What other programming languages are you familiar with? I ask because, (i) if you have *no* previous

7/17/15

Ivan Kizema, Christopher Chang2

6/3/15

Genotype & Variant formats binary mode

By default, the 5th column in the .bim ("A1") is the minor allele and the 6th column (

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Genotype & Variant formats binary mode

By default, the 5th column in the .bim ("A1") is the minor allele and the 6th column (

6/3/15

Rakan, Matt Neville2

5/22/15

Problem with importing data into plink

Hi, When you cut and paste from excel are there any empty cells, ie do you just select the data to be

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Problem with importing data into plink

Hi, When you cut and paste from excel are there any empty cells, ie do you just select the data to be

5/22/15

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