stacks . vcf . admixture , structure extract data from vcf ?

Hi . i have a .vcf file from a radseq project and i would like to do an admixture or structure analysis but i dont understand how i can extract the SNP information from the vcf to do further analysis . the vcf alone should contain all the info i need for this ?

radseq stacks structure

• 1,056 views • link

updated 2.6 years ago by Pierre Lindenbaum

• written 2.6 years ago by csag6433 •

what is "the SNP information" ?

• 0 views • link

written 2.6 years ago by Pierre Lindenbaum

0 answers

No answers yet.

More posts like this

How to extract info of samples of interest from VCF file?
written 3.9 years ago by Qingyang Xiao

Hi, Now I am starting a GWAS project. VCF files have been generated. However, I only need the information of a subset of genotyped individuals …
Convert 70 VCF to PED and MAP plink files
written 5.5 years ago by anithanagaraj93 •

Hi everyone, I have 70 VCF files (1 per region), So need to create PCA plots and Admixture Analysis. I go through the PCA and …
Filter only SNPs in 1000 Genomes Data Slicer
written 5.7 years ago by irieljoerin •

Hi all, I´m trying to retrieve genotypic data from 70 SNPs (from different chromosomes) from certain 1000 Genomes populations. I plan to use Data Slicer …
PASNP genotype data
written 6.5 years ago by Hadi M •

Hi, I would like to know if there is an alternative way to download the genotyping data from the PAN-Asian SNP database (http://www4a.biotec.or.th/PASNP)? I cannot …
Get rsID for a list of SNPs in an entire GWAS sumstats file
written 8.4 years ago by camerond

I have downloaded a GWAS sumstats file and have a list of SNP locations. The information for each SNP location is condensed in column 1 …
Extract SNPs and SNP ID's from vcf file
written 8.8 years ago by aadhirareddy1323 •

Hi all, I have vcf file.I am trying to extract ID ,SNPs and SNP ID's in the following way : It has to conform with …
SNP data filtering from VCF file
written 9.2 years ago by sukesh1411 •

Hi I am sorry although there are so many questions on this query i could not find the relavant answer. I used vcftools to extract …
Convert and filter VCF by a pre-existing BIM
written 9.2 years ago by jlawlor •

Hi all, I'm trying to convert a VCF to PLINK format (BED/BIM/FAM), however I'd like to do so using a fixed, pre-existing BIM file. In …
Extract each annotation in 'info' column in snpEff output
written 10.8 years ago by jan

Hi, I have used snpEff to annotate my vcf file. I previously use Annovar to annotate my vcf file and the fields are nicely separated …
Can I get SNP information by individual from dbSNP
written 11.7 years ago by Chen Sun

Hi all, I download the dbSNP data, both all and common SNP information, which is produced by 1000G project. But I do not want to …