genome version conversion · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

genome version conversion

Hi all

I'm new in population stratification study. I gathered many SNP genotyping data from different microarray genotyping platformes. For this purpose, I must merge all data files in one file for subsequent analysis. So, all genotypes must be in one genome version. Therefore, I'm wondering if it is better to convert all genotypes to the newer genome version or the older one ?

Thanks

genome snp liftover

• 2,052 views • link

updated 4.7 years ago by Ram

• written 12.0 years ago by Myosotis1979 •

1 answer

Should be same version of genome,

• 0 views • link

updated 4.7 years ago by Ram

• written 11.9 years ago by Manvendra Singh

Log in to answer this question.

More posts like this

How to merge SNP datasets aligned to different reference genome versions without re-calling variant…
written 4 months ago by jhonatan.henrique •

I am working with SNP data from two different projects that used different versions of the reference genome. Dataset 1: - 34,566,550 SNPs; - 1987 …
Combine GBS and WGS data for variant calling in GWAS analysis
written 1.7 years ago by behnam •

We have Genotyping-by-Sequencing (GBS) data for 117 Brassica Juncea population and Whole-Genome-Sequence (WGS) data for the two parental genotypes. Since the sequencing platforms are different, …
Can I use a subset of VCF my files for quality checks?
written 5.5 years ago by floortje •

Dear all, I have about 3,500 VCF files (each of approximately 500mb) containing whole-genome sequencing data of 3,500 individuals. The files contain all variants mapped …
merge files with PLINK
written 7.2 years ago by Myosotis1979 •

Dear all I'll greatly appreciate your help/advice regarding merging two sets of data with PLINK. I have a set of SNP genotypes in PLINK format …
Is rs# of an SNP comparable between genome version or build?
written 9.2 years ago by Rashedul Islam

Hi All, I am working on public genotype data in [opensnp][1]. I found that different platform (e.g., 23andme, decodeme etc) uses different genome versions (e.g., …
How to convert and annotate apt-probeset-genotype into PLINK format
written 10.5 years ago by Myosotis1979 •

Dear all, I called SNP genotypes of 100 Affy6 CEL files using apt-probeset-genotype from APT in order to perform a subsequent CNV analysis with PennCNV. …
SNP array genotyping data in cancer
written 12.1 years ago by imagineyd

Hi all :) I'm looking for SNP array genotyping data of cancer patients, especially germ line variants. So, I downloaded lots of SNP data from …
How To Extract A Specific Population Vcf File From 1000G Genotypes Vcf File
written 13.8 years ago by J.F.Jiang

<p>I have downloaded the 20101123 version RAW genotypes data encoded in VCF format. And I want to use plink to calculate the LD relation with …
Remove Linked Markers Before Combining Populations, Or Afterward
written 14.4 years ago by pufferfish

<p>Various population genetics analyses have a requirement that the provided genotypes are only of unlinked markers. This can be easily accomplished with PLINK using the …
Importance Of Consistency Of Downstream Analysis Of Sequence Data
written 15.3 years ago by Pi •

<p>Greetings</p> <p>When a lab performs an investigation to sequence a population of individuals, is it typically the case that every individual in the population will …