結(jié)論
LDhat:不能用來計(jì)算大樣品的重組率。18個樣品，200位點(diǎn)耗時大概一小時；52樣品，200個位點(diǎn)，耗時遙遙無期。
CPLDhat：改進(jìn)后的LDhat，可以使用mpirun進(jìn)行多線程計(jì)算，大大節(jié)省運(yùn)行時間；52樣品，200位點(diǎn)已運(yùn)行5天
Phase：單次只能計(jì)算500個位點(diǎn)，速度慢；52樣品，500個位點(diǎn)，耗時11天。
Mlrho：不能計(jì)算兩兩位點(diǎn)之間的重組率，只能計(jì)算全基因組的重組率，運(yùn)行速度很快。
LDhat
命令行示例
$LDhat_DIR/interval -seq chrA01_1.site -loc chrA01_1.locus -lk Bra.lk -its 1000000 -bpen 5 -samp 2000
input file
- LOCUS文件
- SITE文件
- Lookup文件
CPLDhat
命令行示例
$DIR/mpirun -n 30 $DIR/interval -seq chrA01_3.site -loc chrA01_3.locus -lk Bra.lk -convergence
input file
- CPLDhat 輸入文件格式與LDhat完全一致
- CPLDhat 不需要設(shè)置參數(shù)
- CPLDhat 只是LDhat的基礎(chǔ)上稍微修改，使其能用mpirun多線程運(yùn)行，進(jìn)而提升節(jié)省運(yùn)行時間
Phase
Usage
$DIR/PHASE -MR -X10 chrA01_1.inp chrA01_1.out
*input file *
Phase只有一個輸入文件，其格式如下：
3 ## 3個樣品
5 ## 5個位點(diǎn)
P 300 1313 1500 2023 5635 ##P固定格式，后跟5個位點(diǎn)的具體位置
MSSSM ##M代表該位點(diǎn)為多等位基因，S代表該位點(diǎn)二等位基因。1、5 為多等位位點(diǎn)，2、3、4為二等位位點(diǎn)
#sample1 ##樣品1名字
12 1 0 1 3 ##For multiallelic loci a positive integermust be used for each allele (representing the number of repeats atmicrosatellite loci),and data for each locus should be separated by aspace
11 0 1 0 3 ##For biallelic loci, any two characters (e.g.A/C, G/T, 0/1) can be used to represent the two alleles, and theydo not need to be separated by a space
#sample2
12 1 1 1 2
12 0 0 0 3
#sample3
-1 ? 0 0 2 ##Missing alleles at multiallelic loci should be representedby -1.
-1 ? 1 1 13 ##Missing alleles at SNPloci should be entered as ?
out put
計(jì)算重組率的結(jié)果在_recom文件里
_freqs Estimates of the sample haplotype frequencies (which can alsobe used as estimates of the population haplotype frequencies).The first two columns are self-explanatory. The next 2 columnsgive i) estimates (posterior means) of haplotype frequencies forthe whole sample, and ii) estimated standard deviations (squareroot of the variance of the posterior distribution) for these frequencies. If the -c option is used (see below) then additionalpairs of columns give estimated haplotype frequencies and standard deviations for each group specified in the input file.
_pairs List of the most likely pairs of haplotypes for each individual,together with their probability. Only pairs whose probabilityexceeds the threshold given by the -O flag are listed.
_recom Contains estimates of recombination parameters across the region, using the general model for varying recombination ratefrom Li and Stephens (2003). (Note: these estimates are produced only if the recombination model is used: see the -M option.Also, the estimates have a straightforward interpretion only ifthe positions of the loci are specified in the input file.) Thefirst line of the file gives the positions of the loci in the inputfile (to facilitate subsequent analyses using results in this file).Each subsequent line of the file gives a sample from the posterior distribution of the recombination parameters. The firstcolumn gives estimates of the background recombination rate(more precisely, the value of the population genetics parameterρ, here denoted ρ ˉ). Column 2 gives the factor by which the recombination rate between locus 1 and 2 exceeds the background rate, and, similarly, column i gives the factor by which the ratebetween locus i ? 1 and locus i exceeds the background rate.To get point estimates of these quantities I suggest taking themedian of the results for each column. If you are planning tomake use of the results from this file, then it is advisable to usethe -X option described later (eg -X10 or -X100), to obtain moreaccurate estimates.
_hotspot Contains estimates of recombination parameters if one of thehotspot options is used: see the -M option. The estimates have astraightforward interpretion only if the positions of the loci arespecified in the input file. Each line of the file gives a samplefrom the posterior distribution of the recombination parameters.The first column gives estimates of the background recombination rate (more precisely, the value of the population geneticsparameter ρ ˉ). Column 2 gives the estimated left hand edge ofthe first hotspot, column 3 gives the right-hand edge, and column 4 gives the estimated intensity (the factor by which therecombination rate in the hotspot exceeds the background rate.)If this last column is 1 then this corresponds to no increase inrecombination rate in the “hotspot”. To get point estimates ofthese quantities I suggest examining both the mean and the median of the results for each column. (Histograms of each columncan also be helpful in giving you an idea of the uncertainty andskewness in the posterior.) If you are planning to make use ofthe results from this file, then it is advisable to use the -X option described later (eg -X10 or -X100) to obtain more accurateestimates.
_signif Gives the p-value for a permutation test of the null hypothesisthat the cases and controls are random draws from a commonset of haplotype frequencies (only if the case-control status isspecified for each individual; see the -c option below)).
_monitor The monitor file for the goodness of fit of the estimated haplotypes to the underlying model. It has two columns: the first isthe pseudo-likelihood from Stephens and Donnelly (2003); thesecond is the PAC-B likelihood from Li and Stephens (2003).When comparing behaviour of different runs from different starting points I recommend using the first column, as the secondcolumn can be very dependent on the order of the individuals, which can vary a lot across runs. This file replaces the‘‘temp.monitor’’ file produced by previous versions of PHASE
Mlrho
官方網(wǎng)站，摸我（下載軟件解壓后有詳細(xì)說明文檔）
usage
#format
/gpfs01/duliuwen/BioSoft/MlRho_2.8/Auxiliary_Software/FormatPro_0.5/formatPro Bra.pro
#Compute the genome-wide population mutation rate
/gpfs01/duliuwen/BioSoft/MlRho_2.8/mlRho -M 0 -I
#The -I switch in the last command instructed mlRho to write the likelihoods to the binary file profileDb.lik,see likelihood file
/gpfs01/duliuwen/BioSoft/MlRho_2.8/Auxiliary_Software/InspectPro_0.3/inspectPro profileDb.lik |head -n 10
#To compute ? and ρ as a function of ?, use
/gpfs01/duliuwen/BioSoft/MlRho_2.8/mlRho -m 100 -M 200 >rho
input file
Bra.pro格式示例
>Contig1 ##contig1名字
1 0 0 0 5 ##第一列位點(diǎn)位置，第二列A的個數(shù)，第二列C的個數(shù)，第三列G的個數(shù)，第四列T的個數(shù)
2 1 10 0 0 ## 此文件由bam文件轉(zhuǎn)換而來，官網(wǎng)有格式轉(zhuǎn)換的輔助軟件
>Contig2
5 2 0 7 0
6 12 0 0 0
8 0 10 1 0
