python (65.1k questions)

javascript (44.2k questions)

reactjs (22.7k questions)

java (20.8k questions)

c# (17.4k questions)

html (16.3k questions)

r (13.7k questions)

android (12.9k questions)

Questions - genetics

Issue with map file output from plink

I am working with the vcf file (generated using bcftools) to create a map file using plink software. The command i am using is ./plink --vcf sample.vcf --out sample --recode --allow-extra-chr The ou...
test-img

Tania

genetics

vcf-variant-call-format

map-files

Votes: 0

Answers: 1

Latest Answer

The third column of the map file represents the position of the variants based on the recombination map: https://www.cog-genomics.org/plink/1.9/formats#map This field is optional and I assume your inp...
test-img

Yosuke Tanigawa

Creating maps with pie charts from genetic data

I am doing a population genetics study and working with chloroplast data from an oak species. I have performed a DAPC and found that there are 5 clusters of chloroplast genotypes. I want to make a map...
test-img

Christopher McCarron

r

tidyverse

tmap

genetics

scatterpie

Votes: 0

Answers: 0

Genetic programming: Can we get multiple bit output from each individual(tree) if we provide 5 bit input?

I want to create population of trees using genetic programming. I am using deap python framework. My trees are based on combination of different logic gates and some terminals. I want to provide each ...
test-img

Mujtaba Hassan Saddozai

genetic-algorithm

genetic-programming

genetics

deap

Votes: 0

Answers: 1

Latest Answer

Solution: I think that if I provide 128 bit binary value to one tree (made of and/or/not/xor gates etc) and do bitwise operation on each gate then I might get 128 bit output.
test-img

Mujtaba Hassan Saddozai

How do I install and use PLINK on Linux? Segmentation fault error

I downloaded the plink zip file from the website (https://zzz.bwh.harvard.edu/plink/download.shtml), unzipped, and then execute plink in the working directory. $ unzip plink-1.07-x86_64.zip $ cd plink...
test-img

melolili

segmentation-fault

genetics

Votes: 0

Answers: 1

Latest Answer

You may have some luck with PLINK 1.90: https://www.cog-genomics.org/plink/1.9/ PLINK 1.9 is well maintained and much more efficient compared to PLINK 1.07. Most of the analysis commands in 1.07 are s...
test-img

Yosuke Tanigawa

Posts

Questions

Blogs

Jobs