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, 23:27, 1 July 2015
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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 |
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