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===Converting GWAS Panel Files into VCF ===
===Converting GWAS Panel Files into VCF ===
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.
* '''PLINK:''' Use PLINK2 (available [https://www.cog-genomics.org/plink2 here]) as follows:
plink --bfile Gwas.Chr20.Phased.Output \
--recode vcf \
--out Gwas.Chr20.Phased.Output.VCF.format
* '''MaCH:''' Use Mach2VCF (coming soon) as follows:
mach2VCF --haps Gwas.Chr20.Phased.Output.hap \
--snps Gwas.Chr20.Phased.Output.snps \
--prefix Gwas.Chr20.Phased.Output.VCF.format
* '''SHAPEIT:''' Use SHAPEIT (available [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]) as follows:
shapeit -convert \
--input-haps Gwas.Chr20.Phased.Output \
--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf
= Chromosome X Imputation =
= Chromosome X Imputation =
