550
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
The 1000 Genome pilot project genotypes use NCBI Build 36.
The 1000 Genome pilot project genotypes use NCBI Build 36.
=== Step 1: Phasing ===
=== Step 1: Pre-Phasing ===
For the pre-phasing step we recommend [[MaCH]] using the --phase command line option. As input [[MaCH]] needs a [[Merlin]] format pedigree and data file. All markers must be ordered according to their physical position.
==== Usage ====
mach1 -d sample.dat -p sample.ped --rounds 20 --states 200 --phase --interim 1 --sample 1 --compact
==== Parameters ====
--rounds R
how many iterations of the Markov sampler should be run.
--states ST
use a random subset of ST haplotypes as reference. We recommend values between 200 - 500. More states result in more accurate haplotypes, but are computational more expensive.
--interim I
output a set of best-guess haplotypes every I rounds by building consensus from all previous Markov iterations. These haplotypes can be used for imputation.
--sample SA
output a set of haplotypes every SA rounds based on random sampling from the last Markov iteration. These intermediate results can be combined and used as input for the imputation process.
--phase
enables [[MaCH]] phasing mode.
--compact
reduces the amount of memory needed dramatically, but doubles execution time.
=== Step 2: Imputation ===
=== Step 2: Imputation ===
