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* polymutt2: taking a VCF and the map file generated by vcf2map (the vcf file can be a complete vcf with all variants and samples)
* polymutt2: taking a VCF and the map file generated by vcf2map (the vcf file can be a complete vcf with all variants and samples)
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf
* If parents are available genotypes can be phased by transmission (accuracy is not as good as above)
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --best_path
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --best_path
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --fam_id fam1
* If a single family is desired to be output (the ped file can contain all families but will be ignored)
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --fam_id
* If only a range is desire to output (for example the whole chromosome can be divided into multiple parallel jobs each working on a range)
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --out_range 1:1000000-2000000
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --out_range 1:1000000-2000000
