MaCH

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MaCH (MArkov Chain Haplotyping), mostly known as a software for genotype imputation, is a Hidden Markov Model (HMM) based haplotyper can that reconstruct haplotypes from genotypes of unrelated individuals. Three primary uses of MaCH are (1) to resolve haplotypes from diploid genotypes; (2) impute missing genotypes; and (3) perform disease mapping analysis.

Input Files

Mach takes unphased genotypes of unrelated individuals as input. Two input files are mandatory: a pedigree file and a marker information file. The pedigree file stores five key pieces of information and genotypes for each individual, with missing genotypes accepted and additional phenotypes allowed. The marker information file provides the list of marker names. Note that the list must be in order according to physical positions of the markers along the chromosomes. For more details, refer to http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html.

Pedigree File (mandatory)

Each person contributes to one line in a pedigree file. Required fields are (1) the first five fixed fields corresponding to five key pieces of information (namely: family person father mother sex), and (2) genotype fields. Phenotype fields are allowed inbetween but will not be used by the program.

<sample.ped>

 fam1 indiv1 0 0 1 0/0 2/3 ./. 
 fam2 indiv2 0 0 2 1/2 2/2 1/4 

<EOF sample.ped>

This sample.ped contains 2 individuals. The first individual is from family fam1 with person ID indiv1 and no parental information available (father = 0, mother = 0). This person is a male (sex = 1). His genotypes are missing at the first and third markers (0/0 and ./.), and is 2/3 (C/G) at the second marker. Similarly, the second individual is from family fam2 with person ID indiv2 and no parental information available (father = 0, mother = 0). This person is a female (sex = 2). Her genotypes are 1/2 (A/C) at the first locus, 2/2 (Homozygous for C) at the second locus and 1/4 (A/T) at the third locus.

Marker Information File (mandatory)

<sample.dat>

 M SNP1
 M SNP2
 M SNP3

<EOF sample.dat>

This file tells us that fields 6-8 in the pedigree file store genotypes for SNP1-3 correspondingly. Note again that the list of SNPs must be in their physical order along the chromosomes.


Optional Input files

External/reference files

External/reference (e.g., HapMap) input files (snp and haplotype files) are optional. Mach 1.0 accepts two different formats: MACH format or HapMap format.

MACH format SNP File

One line per SNP and one field (marker name) only.

For example:

marker1
marker2
...
MACH format Haplotype File

One line per haplotype.
Heading identification fields are optional.
Each non-haplotype/heading field shall not start with a numeric digit.

For example:

 H_0001->H_0001 HAPLO1 2332323244332
 H_0001->H_0001 HAPLO2 2332323422132
 H_0002->H_0002 HAPLO1 3332323244332
 H_0002->H_0002 HAPLO2 3311321242332
 ...
HapMap format reference files

HapMap format files can be downloaded from http://hapmap.org/downloads/phasing/2006-07_phaseII/phased/ or http://hapmap.org/downloads/phasing/2007-08_rel22/phased/

HapMap format SNP File: legend file downloaded from HapMap website
HapMap format Haplotype File: phase file downloaded from HapMap website


When using HapMap format files, turn on --hapmapFormat option.

 mach1 -d sample.dat -p sample.ped -s genotypes_chr14_CEU_r21_nr_fwd_legend.txt -h genotypes_chr14_CEU_r21_nr_fwd_phased.gz --hapmapFormat ...

Physical position file

Parameter files

Options

Input Files: --datfile Marker information file for subjects under study. --pedfile Pedigree file for subjects under study.


FAQ

Why and how to perform a 2-step imputation?

A: When one has a large number of individuals (>1000), we recommend a 2-step imputation to speed up.

     A 2-step imputation contains the following 2 steps:

    (step 1) a representative subset of >= 200 unrelated individuals are used to calibrate model parameters; and
    (step 2) actual genotype imputation is performed for every person using parameters inferred in step 1.

      Example command lines for a 2-step imputation:

#step 1:
mach1 -d sample.dat -p subset.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip -r 100 -o par_infer > mach.infer.log
# step 2:
mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log 

Where can I find combined HapMap reference files?

A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html

Where can I find HapMap III / 1000 Genomes reference files?

A: http://www.sph.umich.edu/csg/yli/mach/download/


Does --mle overwrite fed-in genotypes?

A: Yes. But rarely. --mle outputs the most likely genotype guesses by integrating over the probabilities of all possible configurations based on the reference haplotypes. The overwriting happens when the most likely guess differs from the experimental counterpart.

How do I get imputation quality estimates?

A: A simple approach is to use --mask option. For example, --mask 0.02 masks 2% of the genotypes at random, impute them and compare with the masked original to estimate genotypic and allelic error rates. Messages like the following will be generated to stdout:

 Comparing 948352 masked genotypes with MLE estimates ...
 Estimated per genotype error rate is 0.0568
 Estimated per allele error rate is 0.0293 

    A better approach is to mask a small proportion of SNPs (vs. genotypes in the above simple approach). One can generate a mask.dat from the original .dat file by simply changing the flag of a subset of markers from M to S2 without duplicating the .ped file. Post-imputation, one can use   CalcMatch and doseR2.pl to estimate genotypic/allelic error rate and correlation respectively. Both programs can be downloaded from http://www.sph.umich.edu/csg/ylwtx/software.html

    Warning: Imputation involving masked datasets should be performed separately for imputation quality estimation. For production, one should use all available information.


Shall I apply QC before or after imputation? If so, how?

A: Yes. We strongly recommend QC both before and after imputation. Before imputation, we recommend the standard battery of QC filters including HWE, MAF (recommended cutoff is 1% for genotyping-based GWAS), completeness, Mendelian inconsistency etc. Post-imputation, we recommend Rsq 0.3 (which removes >70% of poorly-imputed SNPs at the cost of <0.5% well-imputed SNPs) and MAF of 1%.


How do I get reference files for an region of interest?

A: (1) For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz

    (2) For MACH format, you can do the following:

      (2-1) First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.

      (2-2) Then:

 @ first = `grep -n rsFIRST orig.snps | cut -f1 -d ':'`
 @ last = `grep -n rsLAST orig.snps | cut -f1 -d ':'`

      (2-3) Finally (assuming the third field contains the actual haplotypes, where alleles are separated by nothing):

 awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap

Do I have to sort the pedigree file by physical positions?

A: If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, we strongly recommend sorting the pedigree files.

What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)?

A: mach automatically resets it to maximum possible value.


How is AL1 defined? Which allele dosage is .dose/.mldose counting?

A: AL1 is an arbitrary allele. To be specific, it is the first allele read in the reference haplotypes (file fed to -h or --haps). The earliest versions of mach1 counted the number of AL2 and the latest versions count the number of AL1. One can find out which allele is counted following the steps below.

Take your dosage, geno, and info output (.dose, .geno and .info or .mldose, .mlgeno, and .mlinfo depending on non-mle or mle manner you've used) and check if dosage is the number of AL1 copies or AL2 copies. Example is given below:


 head -1 mldose/chr21.mldose | cut -f3 -d ' ' 
1.962 
head -2 mlinfo/chr21.mlinfo 
SNP Al1 Al2 Freq1 MAF Quality Rsq 
rs885550 2 4 0.9840 0.0160 0.9682 0.0021 
 head -1 mlgeno/chr21.mlgeno | cut -f3 -d ' ' 
2/2 

Based on the three files above, we've confirmed that dosage is the number of AL1 copies: you will only to check for one informative case (i.e, dosage values close to 0 or 2) since it's consistent across all individuals and all SNPs.


Can I used unphased reference?

A: Yes. You simply need a combined pedigree (.ped) and marker information file (.dat).

     For example, if you have:

      ref.hap
      ACGGA
      CCGAA

      ref.snps
      SNP1
      SNP2
      SNP3
      SNP4
      SNP5

      sample.ped
      1 1 0 0 1 A/A G/G 

      sample.dat
      M SNP1
      M SNP4

      The combined files should look like:
      comb.ped
      r1 r1 0 0 1 A/C C/C G/G G/A A/A
      1 1 0 0 1 A/A ./. ./. G/G ./.

      comb.dat
      M SNP1
      M SNP2
      M SNP3
      M SNP4
      M SNP5


More questions?

A: Email Yun Li (yunli@med.unc.edu) or Goncalo Abecasis (goncalo@umich.edu).


Examples

Imputation

 mach1 -d sample.dat -p sample.ped -s hapmap.snps -h hapmap.hap -r 100 -o phase