PopLDdecay

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How the calculated the decay line by nonlinear regression to the LD plot?

3

Hi, I am trying to add the non-linear regression tendency line to the Linkage Disequilibrium (LD) plot. I followed the manual document of PopLDdecay and got the plot. However, I...

sekhwal

RAM Usage and other

2

From my first tries, it seems that what you save in storage (compared to other software) you spend it in RAM. Do you have some tests that show RAM usage...

GabrieleNocchi

In the off chance you'd like to provide users with access to a containerized version of PopLDdecay, I've recently generated a Singularity container. The image is housed on Singularity Hub:...

jlboat

Structure Variation

1

when I use a vcf with structure variation, It's warning skip Indel site, there are total skip Indel sites number is : 618346，after filter Remain SNP Number : 0. Does...

lunky-zao

Confidence intervals

4

Hi, I was wondering how are the confidence intervals calculated for pairwise LD calculation using r^2? My LD calculation corresponds very well with patterns of genetic diversity and recombination rate,...

Homap

When using PopLDdecaly, it will be prompted with “command option error! please check”

1

The code I used was “nohup PopLDdecay -InVCF 74.vcf.gz -MaxDist 100 -MAF 0.1 -Miss 0.2 -OutStat wewLD.stat.gz -SubPop wew.list -OutType 1 1 > o.log 2 > e.log &”, it will...

Biocode-lab