plink-ng

plink-ng copied to clipboard

Request for pgen files to include a version number in the header

8

We (Broad Institute/All of Us) are planning to start generating some large pgen datasets using a pgen writer that we've implemented, and are a bit concerned that the pgen file...

cmnbroad

Request: plink2 --extract/exclude-if-info [key(s)...]

1

Is it possible to implement an improvement to this flag to allow for multiple INFO filters in the initial vcf to pgen conversion? `plink2 --vcf file.vcf --extract-if-info "A == 1"...

kscott-1

how to install in arm64 ? thks

4

zsw-test

CentOs7.9 install plink1.9 error

3

My operating system version is CentOS 7.9, and Plink version is 1.9. I have already executed `yum install -y gcc gcc-c++ libstdc++ gcc-gfortran glibc glibc-devel make blas-devel lapack lapack-devel atlas-devel`,...

gaozejie

Hi Chris, thanks for your constant work on plink. Is there any interest or plan for an upstream Dockerfile for 1.9 & 2.0? For those running analysis in containers, this...

kscott-1

Multithread-only --glm floating point exception

2

Original bug report at https://groups.google.com/g/plink2-users/c/ABcn9tN6ttA .

chrchang

pgenlibr: multi-threading?

1

Hi, I am wondering whether, by default, `pgenlibr` uses multithreading the same way plink2 does? We are comparing performance between pgenlibr and wrapped plink2 calls in R and are seeing...

agilly-regn

`Error: Non-concatenating --pmerge[-list] is under development.`

9

Hi, running Plink (v2.00a4LM AVX2 Intel) errors out when merging multiple datasets. ``` $ ../plink2 --debug --memory 8000 --threads 6 --pmerge-list input_sources.txt --out merged PLINK v2.00a4LM AVX2 Intel (9 Jan...

jacorvar

https://groups.google.com/g/plink2-users/c/0bdSodZJj-w/m/JDve-rBpBQAJ reports a case where there's a different underlying error that's incorrectly suppressed.

chrchang

Plink2 round-tripping vcf->pgen->vcf does not preserve contig names

3

In round tripping vcf- > pgen(pvar/psam) -> vcf, contig names are not preserved: Original VCF (one contig named "chr1"): ``` ##fileformat=VCFv4.2 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO...

cmnbroad