格式轉(zhuǎn)換
hapmap格式：hmp.txt
plink格式：ped和map以及二進制文件bed/bim/fam
vcf格式：vcf
1. hapmap <-> vcf
hapmap -> vcf
run_pipeline.pl -SortGenotypeFilePlugin -inputFile hmp.txt -outputFile test.sort.hmp.txt -fileType Hapmap
run_pipeline.pl -Xmx100g -fork1 -h test.sort.hmp.txt -export -exportType VCF
vcf -> hapmap
run_pipeline.pl -Xms10g -Xmx100g -vcf in.vcf.gz -sortPositions -export out.hmp.txt -exportType HapmapDiploid
2. hapmap_to_qtl2
Convert HapMap file into a useable R qtl2 genotype file
#下載
git clone https://github.com/jlboat/hapmap_to_qtl2.git
#使用
usage: hapmap_to_qtl2.py [-h] --hapmap HAPMAP [--output OUTPUT]
This script was designed to convert a hapmap file into R qtl2 format.
optional arguments:
-h, --help show this help message and exit
--output OUTPUT File name for qtl2 output.
required arguments:
--hapmap HAPMAP The name of the input hapmap file.
3. vcf <-> plink
vcf -> plink
plink --vcf input.vcf --recode --out output --double-id --autosome-num 42
plink --file A --make-bed --out A --autosome-num 42
結(jié)果生成：ped/map以及二進制文件bed/bim/fam
添加--recode參數(shù)將輸出結(jié)果調(diào)整為ped格式
plink -> vcf
plink --bfile binary_fileset --export vcf --out new_vcf
