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SHAPEIT can be used to phase a small number of samples (a reference panel required) as well as a large number of samples (NO reference panel required). The reference panels and genetic map files are available for download on their [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html home-page].
SHAPEIT can be used to phase a small number of samples (a reference panel required) as well as a large number of samples (NO reference panel required). The reference panels and genetic map files are available for download on their [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html home-page].
* The following example shows a typical SHAPEIT command line to phase a large number of GWAS samples (<code>Gwas.chr20.Unphased.vcf</code> is the quality control GWAS data set in VCF format).
* The following example shows a typical SHAPEIT command line to phase a LARGE number (>200) of GWAS samples (<code>Gwas.chr20.Unphased.vcf</code> is the quality control GWAS data set in VCF format).
shapeit -V Gwas.chr20.Unphased.vcf \
shapeit -V Gwas.chr20.Unphased.vcf \
-M genetic_map_chr20.txt \
-M genetic_map_chr20.txt \
-O Gwas.Chr20.Phased.Output
* The following example shows a typical SHAPEIT command line to phase a SMALL number (<200) of GWAS samples (<code>Gwas.chr20.Unphased.vcf</code> is the quality control GWAS data set in VCF format).
## The following step splits out variants mis-aligned between the reference and target/gwas panel
shapeit -check \
-V Gwas.chr20.Unphased.vcf\
-M genetic_map_chr20.txt \
--input-ref reference.haplotypes.gz reference.legend.gz reference.sample \
--output-log gwas.alignments
## The following step phases target/gwas panel using the reference panel while excluding the markers found in the step above.
shapeit -B gwas \
-V Gwas.chr20.Unphased.vcf \
--input-ref reference.haplotypes.gz reference.legend.gz reference.sample \
--exclude-snp gwas.alignments.strand.exclude \
-O Gwas.Chr20.Phased.Output
-O Gwas.Chr20.Phased.Output
