MaCH

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 ...

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?

If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, you will probably avoid problems by including markers in the pedigree file sorted in chromosome order.

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

Mach will automatically change this to the maximum possible value.

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

A: AL1 is an arbitrary allele. Typically, it is the first allele read in the reference haplotypes (file fed to -h or --haps). The earliest versions (prior to April 2007) of mach counted the expected number copies of AL2 and more recent versions count the number of AL1. One can find out which allele is counted following the steps below.

1. . First, find the two alleles for one of the markers in your data

 prompt> head -2 mlinfo/chr21.mlinfo 
 SNP      Al1 Al2 Freq1   MAF    Quality  Rsq 
 rs885550 2   4   0.9840  0.0160  0.9682  0.992

1. . Second, check the dosage for a few individuals at this SNP.

 prompt> head -3 mldose/chr21.mldose | cut -f3 -d ' ' 
 1.962 
 1.000
 0.078

1. . Finally, compare these dosages to genotypes.

 prompt> head -1 mlgeno/chr21.mlgeno | cut -f3 -d ' ' 
 2/2 
 2/4
 4/4

In this example, you can see that the first individual has a high dosage count (1.962) and most likely genotype 2/2. The last individual has a low dosage count and most likely genotype 4/4. Thus, the output corresponds to version of Mach released after April 2007, which should tally allele 1 counts.

Note that, on the example above, .mldose could be replaced with .dose and .mlgeno could be replaced with .geno.

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 could create pedigree (.ped) and data files (.dat) that include both reference panel and sample genotypes or request that MaCH merge apppropriate files on the fly.

For example, if you have:

reference.dat

M SNP1
M SNP2
M SNP3
M SNP4
M SNP5

reference.ped

REF1 REF1 0 0 1 A/C C/C G/G G/A A/A

sample.dat

M SNP1
M SNP4 

sample.ped

1 1 0 0 1 A/A G/G

Your could create a combined data set as:

comb.dat

M SNP1
M SNP2
M SNP3
M SNP4
M SNP5

comb.ped REF1 REF1 0 0 1 A/C C/C G/G G/A A/A

  1    1 0 0 1 A/A ./. ./. G/G ./. 

Equivalently, you could write -d reference.dat,sample.dat -p reference.ped,sample.ped on the command line and MACH would merge both files on-the-fly.

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