plink-ng

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Logging bug in bmerge

2

[See two small datasets attached](https://github.com/chrchang/plink-ng/files/4561217/Report.zip). I'm running merge-mode 6 and would thus expect the ordering of the datasets not to matter but I get different results as highlighted in bold...

andrew-slater

--check-sex is depleted in Plink2.0?

1

Hi Chang, It seems that PLINK 2.0 depleted the function for checking sex using inbreeding coefficient. Is there any way in PLINK 2.0 to impute sex from the genotypes? PLINK...

SiyangLiu

Multi-variate test in Plink

1

Hi Chang, Does Plink support multiple phenotype association test? Best, Siyang

SiyangLiu

--clump

1

I am wondering it would be very useful to add a log10(p)-like option to --clump-p which would save some effort to prepare for a P column when it is very...

jinghuazhao

**tl;dr - it would be useful if there were an option for using D' instead of correlation for --flip-scan.** --flip-scan is a useful tool in quality control for identifying flipped...

JoniColeman

Hi, I called CNV using GenomeSTRiP software, I analyzed the CNV data via plink(v1.07) --gfile command, and in the only results plink.gvar.summary FIELD and VALUE columns , what is the...

Jingjiao-ma

Consider using different versions when new releases are made

2

I am assisting a user to use plink2 on our HPC cluster and your versioning course issues for us. i.e. using the same version for different releases and distinguish them...

Sabryr

Unjustified NA output?

2

Hello and thanks for the work! We've been looking at various association tools. Based on the code, it looks like PLINK2 computes the logistic regression model using a Cholesky decomposition...

apoliakov

hi I run plink v1.07 Association mapping with segmental CNV data: regional tests the EMP1 and EMP2 of every region is 1 my vcf is ``` #CHROM POS ID REF...

Jingjiao-ma

What is the multiple correction method used in CNV region-based assco

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Hi Christopher, I have got some CNV results for about 1000 samples, and I followed the instructions http://zzz.bwh.harvard.edu/plink/cnv.shtml#reg-assoc on the website to perform a region-based association test. In the result...

ruqianl