search

BGI-shenzhen / LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
MIT License
134 stars 40 forks source link

Dose this tool need phenotypes? #21

Closed Alice-yyt closed 8 months ago

Alice-yyt commented 2 years ago

Hello every, I conduct the commend: LDBlockShow -InVCF aln_sorted2.vcf -OutPut out -Region NC_001802.1:1:2000 -OutPng -SeleVar 2 and got the result: #Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :15

Start Region Cal... :NC_001802.1 1 2000; In This Region TotalSNP Number is 207

find blocks... Warning: Skipping --blocks, since there are less than two founders with nonmissing phenotypes. (--make-founders may come in handy here.) mv: cannot stat ‘out.plink.blocks.det’: No such file or directory gzip: out.blocks: No such file or directory Can't locate SVG.pm in @INC

I don’t why I got this warnings. What information should we provide in the vcf file for LDBlockShow?

Thank you

hewm2008 commented 2 years ago

@Alice-yyt
A: the SVG.pm : I think it's because of your incomplete download. you can redownload the soft , Dir [bin/svg_kit] must be exists . B : you can change the blocks method by add para [ -BlockType 2 ] . or see more at : https://www.biostars.org/p/205746/