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An example command for ''de novo'' mutation detection using a different parameter setup (higher mutation rate) is as follows:
An example command for ''de novo'' mutation detection using a different parameter setup (higher mutation rate) is as follows:
polymutt -p input.ped -d input.dat -g input.gif --denovo --rate_denovo 1.2e-06 --out_vcf out.denovo.vcf --nthreads 4
polymutt -p input.ped -d input.dat -g input.gif --denovo --rate_denovo 1.2e-06 --out_vcf out.denovo.vcf --nthreads 4
Examples of calling X, Y and MT:
polymutt -p input.ped -d input.dat -g input.gif --out_vcf out.vcf --chrX X --chrY Y --MT MT --nthreads 4
polymutt -p input.ped -d input.dat --in_vcf input.vcf --out_vcf out.vcf --chrX X --chrY Y --MT MT --nthreads 4
== Input files ==
== Input files ==
