使用ShapeIT2进行单倍型分型

ShapeIT2支持两种phasing的方法 (for unrelated individuals without family information)

• 使用参考面板

• 不使用参考面板

输入文件都是VCF文件。

步骤：

1. 将VCF按照染色体分开

   vcftools --gzvcf chinese-han.phase3.genotypes.vcf.gz \
            --chr 22 \
            --recode \
            --recode-INFO-all \
            --remove-filtered-all \
            --min-alleles 2 \
            --max-alleles 2 \
            --out chinese_chr22

2. phasing

   1. 不使用参考面板

      shapeit --input-vcf gwas.vcf \
              -M genetic_map.txt \
              -O gwas.phased \
              -T 4

   2. 使用参考面板

      使用1000G作为参考面板。

      1. Check SNP between INPUT and REF PANEL

         shapeit -check \
                 --input-vcf test_chr22.recode.vcf \
                 -M ~/one_thousand_genome/1000GP_Phase3/genetic_map_chr22_combined_b37.txt \
                 --input-ref ~/one_thousand_genome/1000GP_Phase3/1000GP_Phase3_chr22.hap.gz \
                 ~/one_thousand_genome/1000GP_Phase3/1000GP_Phase3_chr22.legend.gz \
                 ~/one_thousand_genome/1000GP_Phase3/1000GP_Phase3.sample \
                 --output-log test_chr22.alignments

      2. Phase wirh REF (exclude SNPs in .strand.exclude)

         shapeit --input-vcf test_chr22.recode.vcf \
                 -M ~/one_thousand_genome/1000GP_Phase3/genetic_map_chr22_combined_b37.txt \
                 --input-ref ~/one_thousand_genome/1000GP_Phase3/1000GP_Phase3_chr22.hap.gz \
                 ~/one_thousand_genome/1000GP_Phase3/1000GP_Phase3_chr22.legend.gz \
                 ~/one_thousand_genome/1000GP_Phase3/1000GP_Phase3.sample \
                 -O test_chr22.phased.with.ref \
                 --exclude-snp test_chr22.alignments.snp.strand.exclude \
                 -T 4