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You can increase accuracy of SHAPEIT by increasing the number of conditioning states on which haplotype estimation is based. By default, SHAPEIT uses 100 states per SNP across the dataset which gives good accuracy while maintaining reasonable running times. The complexity of the algorithm is linear with the number of conditioning states, so feel free to increase this number if your computational resources allow it. For instance, if you set this number to 200, it will take times longer than with 100 states. You can set the number of conditioning states with the --states option as follows:
A phase informative read (PIR) is a sequencing read that span at least 2 heterozyguous sites. In the following, we require first that the sequence data is stored in BAM files and second that the genotype data to be phased is in VCF format. We developed a small tool, extractPIRs, to extract the PIRs from BAM files that relies on the samtools API for efficiency. You can download it from here:
First, download the source code of makeBGLCHUNKS from here. Then, compile by typing make in the terminal. Note that compilation needs a recent version of boost libraries. This piece of software builds a file from a given VCF that contains the chunk coordinates required to run Beagle 4 in each chunk. Feed makeBGLCHUNKS with GLs.vcf.gz and two parameters:
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