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zhangrui2018@picb.ac.cn
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toydata/
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‎toydata/Summary_Statistics/input.region‎

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a 1 100 350

‎toydata/Summary_Statistics/input.vcf‎

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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Ind1 Ind2 Ind3 Ind4 Ind5
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1 100 . A T . . . GT 0|1 0|0 0|0 1|0 0|0
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1 110 . G T . . . GT 0|1 0|0 0|0 1|0 0|0
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1 120 . A C . . . GT 1|1 1|1 1|1 1|1 1|1
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1 130 . A T . . . GT 0|0 0|0 0|0 0|0 0|0
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1 140 . G T . . . GT 0|1 0|0 0|0 0|0 0|0
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1 150 . G T . . . GT 0|0 0|0 1|0 0|1 0|0
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1 160 . A G . . . GT 0|0 0|0 0|0 0|0 0|0
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1 170 . A C . . . GT 0|0 0|0 0|0 0|0 0|0
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1 180 . A G . . . GT 0|0 0|0 0|0 0|0 0|0
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1 190 . G A . . . GT 1|1 0|1 1|1 1|1 1|1
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1 200 . A G . . . GT 1|0 0|0 0|0 0|0 0|0
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1 210 . A T . . . GT 0|0 1|0 0|0 0|0 0|0
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1 220 . A C . . . GT 1|0 0|1 1|0 0|1 1|0
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1 230 . C G . . . GT 0|0 0|0 0|0 0|0 0|0
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1 240 . C T . . . GT 0|0 0|0 0|0 0|0 0|0
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1 250 . T G . . . GT 1|0 0|1 1|0 0|1 1|0
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1 260 . T C . . . GT 1|1 1|1 1|1 1|1 1|1
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1 270 . G T . . . GT 0|0 0|0 0|0 0|0 0|0
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1 280 . G C . . . GT 0|0 0|0 0|0 0|0 0|0
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1 290 . T A . . . GT 0|0 0|0 0|0 0|0 0|0
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1 300 . C T . . . GT 0|0 0|0 0|0 0|0 0|0
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1 310 . A C . . . GT 0|0 0|0 1|0 0|1 0|0
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1 320 . T A . . . GT 0|0 0|0 0|0 0|0 0|0
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1 330 . T C . . . GT 0|0 0|0 1|0 0|1 0|0
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1 340 . T G . . . GT 0|0 0|0 1|0 0|1 0|0
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1 350 . G T . . . GT 0|0 0|1 0|0 0|0 1|0

‎toydata/Summary_Statistics/output.stat‎

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regionID chr start end #sequence #marker ThetaPI ThetaK #segregating #haplotype Hap_diversity Dtajima Dtajima_P Dtajima_adj.P
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a 1 100 350 10 26 4.4 4.5953149109272 13 7 0.9333333333333333 -0.193407676442191 0.896843046548428 0.896843046548428

‎toydata/Summary_Statistics/readme‎

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calculate the following statistics within given regions:
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1.number of sequence
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2.number of genetic markers
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3.number of singleton
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4.ThetaPI
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5.ThetaK
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6.number of segregating site
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7.number of haplotype
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8.Haplotype diversity
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9. Tajima's D (with p-values and BH-corrected P-values)
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input:
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1. phased VCF file [required]
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2. target regions to be analyzed [required]
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3. samples to be included [optional, default = 'all']
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4. length of sliding windows (bp) and increment [optional, default = 'target_region']
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5. name of output file [optional, default = 'out']
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output:
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*.stat
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parameter:
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--vcf: input vcf file
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--region: region file, 4 columns: <region ID> <chrom ID> <start pos> <end pos>, no header line, tab or space separated
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--samples: included sample ID list
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--window_shift: windowsize@increment
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--out: prefix of output file
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commands line for example data:
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python Summary_Statistics.py --vcf input.vcf --region input.region --out output

‎toydata/example1/.nfs0000001656dc040300059e4f‎

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AdmixSim 2
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Arguments and Options:
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Modfile = test.mod
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SNVfile = test.snv
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Hapfile = test.hap
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Indfile = test.ind
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Output population list and corresponding generation and population size: Admixed 8g 4;
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Seed = 1598518282
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Chr = A
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Recombinaion Setting: Using position-specific genetic distance in snv file
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Mutation Setting: General mutation rate = 1e-08
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Out prefix = out1
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==========================================================================================================
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Simulation start! Thu Aug 27 16:51:22 2020
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Reading snvfile time: 0s
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Reading indfile time: 0s
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Reading modfile time: 0s
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Reading hapfile time: 0s
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Simulation time: 0s
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Saving ancestral sequence data time: 0s
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Final add de novo mutation and output snvfile time: 0.01s
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Population Admixed at generation 8 output time: 0s
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Simulation end! Thu Aug 27 16:51:23 2020
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‎toydata/example1/out1.af‎

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Gen Pop Position(s) Condition Frequency Male_Frequency Female_Frequency

‎toydata/example1/out1.hap‎

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00100000011010011000000000
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11101000010000001000000000
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00100000000100001000000000
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00100000010010011000000001
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00100100010010011000010110
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00100000010000001000000000
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11100000010000001000000000
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00100100010010011000010110

‎toydata/example1/out1.ind‎

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Ind1 Admixed_8 0
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Ind2 Admixed_8 0
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Ind3 Admixed_8 0
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Ind4 Admixed_8 0

‎toydata/example1/out1.log‎

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AdmixSim 2
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Arguments and Options:
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Modfile = test.mod
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SNVfile = test.snv
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Hapfile = test.hap
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Indfile = test.ind
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Output population list and corresponding generation and population size: Admixed 8g 4;
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Seed = 1599362113
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Chr = A
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Recombinaion Setting: Using locus-specific genetic distance in snv file
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Mutation Setting: Uniform mutation rate = 1e-08
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Out prefix = out1
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==========================================================================================================
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Simulation start! Sun Sep 6 11:15:13 2020
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Reading snvfile time: 0s
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Reading indfile time: 0s
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Reading modfile time: 0s
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Reading hapfile time: 0s
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Simulation time: 0s
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Saving ancestral sequence data time: 0s
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Final add de novo mutation and output snvfile time: 0s
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Population Admixed at generation 8 output time: 0s
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Simulation end! Sun Sep 6 11:15:13 2020
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‎toydata/example1/out1.seg‎

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Ind1 Hap 1
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16469059 0.02114202 23976120 0.2125382477 Anc1
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23976120 0.2125382477 47601123 0.6243576526 Anc2
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47601123 0.6243576526 48849346 0.66376859 Anc1
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Ind1 Hap 2
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16469059 0.02114202 36275930 0.4250721252 Anc4
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36275930 0.4250721252 37634829 0.455307771 Anc2
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37634829 0.455307771 46661084 0.6041259271 Anc4
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46661084 0.6041259271 47601123 0.6243576526 Anc2
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47601123 0.6243576526 48849346 0.66376859 Anc1
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Ind2 Hap 1
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16469059 0.02114202 32449091 0.3657696056 Anc1
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32449091 0.3657696056 48849346 0.66376859 Anc4
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Ind2 Hap 2
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16469059 0.02114202 17439688 0.04906685992 Anc1
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17439688 0.04906685992 48849346 0.66376859 Anc2
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Ind3 Hap 1
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16469059 0.02114202 48849346 0.66376859 Anc2
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Ind3 Hap 2
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16469059 0.02114202 17169157 0.04128372665 Anc2
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17169157 0.04128372665 28162591 0.3167143957 Anc1
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28162591 0.3167143957 48849346 0.66376859 Anc4
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Ind4 Hap 1
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16469059 0.02114202 20281233 0.1199932635 Anc4
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20281233 0.1199932635 28162591 0.3167143957 Anc1
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28162591 0.3167143957 48849346 0.66376859 Anc4
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Ind4 Hap 2
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16469059 0.02114202 16710569 0.02809022378 Anc1
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16710569 0.02809022378 48849346 0.66376859 Anc2

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