Changes

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 (>200) 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 controlled GWAS data set in VCF format).

  shapeit -V Gwas.chr20.Unphased.vcf \

  shapeit -V Gwas.chr20.Unphased.vcf \

         -O Gwas.Chr20.Phased.Output

         -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 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 controlled GWAS data set in VCF format).

  ## The following step splits out variants mis-aligned between the reference and target/gwas panel

  ## The following step splits out variants mis-aligned between the reference and gwas panel

  shapeit -check \

  shapeit -check \

         -V Gwas.chr20.Unphased.vcf\

         -V Gwas.chr20.Unphased.vcf\

         --input-ref reference.haplotypes.gz reference.legend.gz reference.sample \

         --input-ref reference.haplotypes.gz reference.legend.gz reference.sample \

         --output-log gwas.alignments

         --output-log gwas.alignments

  ## The following step phases target/gwas panel using the reference panel while excluding the markers found in the step above.

  ## The following step phases gwas panel using the reference panel while excluding the markers found in the step above.

  shapeit -B gwas \

  shapeit -B gwas \

         -V Gwas.chr20.Unphased.vcf \

         -V Gwas.chr20.Unphased.vcf \