480
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Download
== NOTE ==
If you are interested in calling '''''de novo''''' mutations in '''trios''' based on '''VCF''' files, we recommend our new tool, triodenovo, which implemented a nicer algorithm with a more natural interpretation of the ''''''de novo''''' quality. Please check it out following the link below. Thanks for trying it out!
http://genome.sph.umich.edu/wiki/Triodenovo
== Updates ==
== Updates ==
The latest version of 0.16 is available for [[#Download | Download]].
The latest version of 0.18 is available for [[#Download | Download]].
v0.18 fixed a bug when it reported inbreeding for some pedigrees which are not inbreeding families
v0.17 fixed a bug when some of the samples in the per files are not in the input vcf file
v0.16 fixed a bug when the input is a VCF file with multiple nuclear families and the ped file contains only a single nuclear family.
v0.16 fixed a bug when the input is a VCF file with multiple nuclear families and the ped file contains only a single nuclear family.
polymutt -p input.ped -d input.dat --in_vcf input.vcf --out_vcf out.vcf --nthreads 4
polymutt -p input.ped -d input.dat --in_vcf input.vcf --out_vcf out.vcf --nthreads 4
Examples for ''de novo'' mutation detection from GLF input files
Examples for ''de novo'' mutation detection
polymutt -p input.ped -d input.dat -g input.gif --denovo --out_vcf out.denovo.vcf --nthreads 4
polymutt -p input.ped -d input.dat -g input.gif --denovo --out_vcf out.denovo.vcf --nthreads 4
polymutt -p input.ped -d input.dat -g input.gif --out_vcf out.vcf --denovo
polymutt -p input.ped -d input.dat -g input.gif --out_vcf out.vcf --denovo
== Download ==
== Download ==
The latest version of source code v0.16 with test files can be [[Media:Polymutt.0.16.tar.gz | downloaded]] here.
The latest version of source code v0.18 with test files can be [[Media:Polymutt.0.18.tar.gz | downloaded]] here.
== Contact ==
== Contact ==
