Latest revision as of 23:32, 30 January 2015

Introduction

This wiki-page explains the main tools available to convert other format files to VCF format.

Use PLINK2 (available here) as follows:

plink --bfile Gwas.Chr20.Phased.Output \
      --recode vcf \
      --out Gwas.Chr20.Phased.Output.VCF.format

Use Mach2VCF (available here) as follows:

mach2VCF --haps Gwas.Chr20.Phased.Output.hap \
         --snps Gwas.Chr20.Phased.Output.snps \
         --prefix Gwas.Chr20.Phased.Output.VCF.format

Use SHAPEIT (available here) as follows:

shapeit -convert \
        --input-haps Gwas.Chr20.Phased.Output \
        --output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf

There are a few pages in this Wiki that may be useful to for Minimac3 users. Here are links to a few:

In case of any queries and bugs please contact Sayantan Das.

@@ Line 1: / Line 1: @@
 = Introduction =
-After the pre-phasing has been done, we can begin to run the imputation. But before that, we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format files). If pre-phased GWAS data is available in VCF format, users can skip this step. Otherwise, the following steps show how to convert other format files to VCF format.
+This wiki-page explains the main tools available to convert other format files to VCF format.
 = Convert '''PLINK''' Files =
@@ Line 13: / Line 13: @@
 = Convert '''MaCH''' Files =
-Use Mach2VCF (coming soon) as follows:
+Use Mach2VCF (available [ftp://share.sph.umich.edu/minimac3/Mach2VCF.v1.Source.Binary.tar.gz here]) as follows:
   mach2VCF --haps Gwas.Chr20.Phased.Output.hap \