MixSIH
MixSIH solves the haplotype assembly problem with mixture model.
Version 1.0.0 (20/03/12)
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Download
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MixSIH can be downloaded from the arrow mark referenced at the bottom of this page.
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Data
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For real data, we used the SNP fragments of Duitama's group [1] and it was downloaded from http://owww.molgen.mpg.de/~genetic-variation/SIH/data/ .
As the correct haplotypes, we used the haplotypes which are determined by pedigree genotypes and we downloaded these from 1000 Genomes Project (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/rele
ase/2010_07/trio/snps/CEU.trio.2010_03.genotypes.vcf.gz)
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Reference
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Matsumoto, H., & Kiryu, H. (2013). MixSIH: a mixture model for single individual haplotyping. BMC Genomics, 14(Suppl 2), S5. [PubMed]
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Slide
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Building
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tar -xzvf MixSIH.tar.gz
cd MixSIH
make
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Running MixSIH
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Usage:
./MixSIH <Option> <Input_file> <Output_file1> <Output_file2>
Options:
-a DOUBLE : Error rate. By default, it is set to 0.1.
Example of running MixSIH
./MixSIH -a 0.05 frag_sample.txt profile.txt haplotype.txt
Format of Input_file:
The first line describes the number of lines of Input_file (which corresponds to the number of SNP fragments - 1).
After first line, each line describes a SNP fragment as below.
\segment_num \fragment_name \start_site1 \sequence1 \start_site2 \sequence2.....
where \segment_num is the number of the segments which don't have gaps in the segments,
\fragment_name is the name of the fragment,
\start_allele'i' is the first site's position of i-th segment (1-origin),
\sequence'i' is the sequence of i-th segment.
The fragments must be sorted by the value of the third column and these can be sorted as follows:
sort -n -k 3 frag.txt > frag_sorted.txt
Example of Input_file:
16
1 frag1 1 000
1 frag2 1 0001
2 frag3 1 11 4 111
2 frag4 2 11 5 11
1 frag5 3 000
1 frag6 4 000000
1 frag7 4 1111
3 frag8 5 11 8 1 10 1
1 frag9 6 000
1 frag10 7 0000
1 frag11 7 1011
1 frag12 7 111
1 frag13 8 010
1 frag14 9 11
1 frag15 9 00
Format of Output_file1:
The Output_file1 is composed of the list of the blocks.
Each block contains a header which is composed of the relative position of the first site,
the number of the sites in the block and the number of the sites which can be phased.
Each block consists of columns as follows:
Col1: relative position of the site
Col2: probability that the phase is (0,1)
Col3: probability that the phase is (1,0)
Col4: exp(connectivity) of the site
Example of Output_file1:
BLOCK: offset: 1 len: 10 phased: 10
1 0.127 0.873 0.000
2 0.102 0.898 4.424
3 0.102 0.898 7.351
4 0.224 0.776 6.891
5 0.072 0.928 10.566
6 0.072 0.928 11.954
7 0.073 0.927 11.126
8 0.166 0.834 12.211
9 0.149 0.851 8.469
10 0.078 0.922 7.296
********
Format of Output_file2:
The Output_file2 is composed of the list of the blocks.
Each block contains a header which is composed of the relative position of the first site,
the number of the sites in the block, the number of the sites which can be phased.
Each block consists of columns as follows:
Col1: relative position of the site
Col2: allele in the first haplotype
Col3: allele in the second haplotype
Example of Output_file2:
BLOCK: offset: 1 len: 10 phased: 10
1 0 1
2 0 1
3 0 1
4 0 1
5 0 1
6 0 1
7 0 1
8 0 1
9 0 1
10 0 1
********
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Extract reliable regions
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extract_reliable_region.rb divides the haplotypes so that MC of the divided regions are higher than threshold.
Usage:
ruby extract_reliable_region.rb <Input_file1> <Input_file2> <Output_file1> <Output_file2> <threshold>
Example:
ruby extract_reliable_region.rb profile.txt haplotype.txt profile_6.txt haplotype_6.txt 6.0
Format of Input_file1 and Output_file1:
It is the same format of Output_file1 of MixSIH.
Format of Input_file2 and Output_file2:
It is the same format of Output_file2 of MixSIH.
[1] Duitama, Jorge, et al. "Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques." Nucleic acids research 40.5 (2012): 2041-2053.