View source for Safv3

We decided to update the native simple binary double format to a much more intelligent format that allows for random access. The format is described in doc/formats.pdf.

This page will contain the impact of this new format in downstream analysis.


=One population analysis=

<pre>
#old master
angsd version: 0.801-27-ga699b44 (htslib: 1.2.1-62-g35746af) build(May  5 2015 03:38:17)
#new new saf
angsd version: 0.801-54-gcf1a12d-dirty (htslib: 1.2.1-62-g35746af) build(May  6 2015 23:34:27)

##old
../master/angsd -anc hg19ancNoChr.fa -dosaf 1 -b /space/genomes/1000g/lowC2014/filelists/ceu.ricco.list -gl 1 -P 5 -out oldceu -rf rf
../master/misc/realSFS oldceu.saf 36 -nSites 213376207 -P 20 >oldceu.saf.ml

##new
../angsd/angsd -anc hg19ancNoChr.fa -dosaf 1 -b /space/genomes/1000g/lowC2014/filelists/ceu.ricco.list -gl 1 -P 5 -out newceu -rf rf
../angsd/misc/realSFS ../nsfs/newceu.saf.idx -P 16 -r 1 >ceu.chr1

##comparison
a<-exp(scan("newceu.saf.idx.chr1.ml"))
b<-exp(as.numeric(read.table("oldceu.saf.ml")[1,]))
a-b
 [1]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
 [6]  0.000000e+00  0.000000e+00 -1.248518e-10  4.059244e-10 -3.843052e-10
[11]  4.952888e-10 -2.465176e-10  7.169737e-11  0.000000e+00  0.000000e+00
[16]  0.000000e+00  0.000000e+00 -4.288667e-11  0.000000e+00  0.000000e+00
[21]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
[26]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
[31]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
[36]  0.000000e+00  0.000000e+00
range(a-b)
[1] -3.843052e-10  4.952888e-10
 barplot(rbind(a,b)[,-c(1,37)],be=T,legend=c("new","old"),col=1:2)
</pre>

==Two population analysis==
<pre>
##old version required a run for each population, to find the intersect and then limit the analysis to the intersect.
##Here are all 4 commands
==> oldceu2.arg <==
../master/angsd -anc hg19ancNoChr.fa -dosaf 1 -b /space/genomes/1000g/lowC2014/filelists/ceu.ricco.list -gl 1 -P 5 -out oldceu2 -rf rf -sites intersect.txt 
==> oldceu.arg <==
../angsd/angsd -anc hg19ancNoChr.fa -dosaf 1 -b /space/genomes/1000g/lowC2014/filelists/ceu.ricco.list -gl 1 -P 5 -out oldceu -rf rf 
==> oldyri2.arg <==
../master/angsd -anc hg19ancNoChr.fa -dosaf 1 -b /space/genomes/1000g/lowC2014/filelists/yri.ricco.list -gl 1 -P 5 -out oldyri2 -rf rf -sites intersect.txt 
==> oldyri.arg <==
../angsd/angsd -anc hg19ancNoChr.fa -dosaf 1 -b /space/genomes/1000g/lowC2014/filelists/yri.ricco.list -gl 1 -P 5 -out oldyri -rf rf

##with intersect found like
gunzip -c oldceu.saf.pos.gz oldyri.saf.pos.gz|sort  -S 50%|uniq -d|sort -k1,1  -S 50% >intersect.txt


##The old saf files are very big so we had to limit the analysis to 180mio sites
../master/misc/realSFS 2dsfs oldceu2.saf oldyri2.saf 36 52 -nSites 180000000 -P 20 >oldceu2.oldyri2.ml

##the new format is much simpler here we simply did
==> newceu.arg <==
../angsd/angsd -anc hg19ancNoChr.fa -dosaf 1 -b /space/genomes/1000g/lowC2014/filelists/ceu.ricco.list -gl 1 -P 5 -out newceu -rf rf 
==> newyri.arg <==
../angsd/angsd -anc hg19ancNoChr.fa -dosaf 1 -b /space/genomes/1000g/lowC2014/filelists/yri.ricco.list -gl 1 -P 5 -out newyri -rf rf

../angsd/misc/realSFS ../nsfs/newceu.saf.idx ../nsfs/newyri.saf.idx -P 32 -r 1 >ceu.yri.chr1.180mb
</pre>

==2 population analysis with simulated data==
After doing this analysis I noticed that I had put a zero too much on the -reglen option for the simulated data with invariable sites. And still the method works fine.
The result is that we still find the sfs nicely eventhough we only have 1/10 of the variability that we would expect from human data. So this is very good.

<pre>
##angsd new: 	->-> angsd version: 0.801-51-g156039a (htslib: 1.2.1-69-gb79f40a) build(May  7 2015 15:31:53)
##angsd old: 	-> angsd version: 0.801-27-ga699b44 (htslib: 1.2.1-69-gb79f40a) build(May  7 2015 15:30:06)

norm <- function(x) x/sum(x)
if(FALSE){
  ##generate data DONT RUN
   if(FALSE){
       ##simulate data with msms
       nRep <- 10
       nPop1 <- 24
       nPop2 <- 16
       cmd <- paste("msms -ms",nPop1+nPop2,nRep,"-t 930 -r 400 -I 2",nPop1,nPop2,"0 -g 1 9.70406 -n 1 2 -n 2 1 -ma x 0.0 0.0 x -ej 0.07142857 2 1  >msoutput.txt ",sep=" ")
       system(cmd)
       ##system("msms -ms 40 1 -t 930 -r 400 -I 2 20 20 0 -g 1 9.70406 -n 1 2 -n 2 1 -ma x 0.0 0.0 x -ej 0.07142857 2 1  >msoutput.txt  ")
       
       source("readms.output.R")
   }
   if(FALSE){
       ##use R to calculate SFS for each pop and 2dsfs
       source("../R/readms.output.R")
       a<- read.ms.output(file="msoutput.txt")
       
       p1.d <- unlist((sapply(a$gam,function(x) colSums(x[1:nPop1,]))))
       p2.d <- unlist((sapply(a$gam,function(x) colSums(x[-c(1:nPop1),]))))
       par(mfrow=c(1,2))
       barplot(table(p1.d))
       barplot(table(p2.d))
       
       sfs.2d <- sapply(0:nPop1,function(x) table(factor(p2.d[p1.d==x],levels=0:nPop2)))
   }
   if(FALSE){
       ##generate ANGSD inputfiles without invariable sites and run it
       system("../misc/msToGlf -in msoutput.txt -out raw -singleOut 1 -regLen 0 -depth 8 -err 0.005")
       system("../misc/splitgl raw.glf.gz 20 1 12 >pop1.glf.gz")
       system("../misc/splitgl raw.glf.gz 20 13 20 >pop2.glf.gz")
       system("echo \"1 250000000\" >fai.fai")
       system("../angsd -glf pop1.glf.gz -nind 12 -doSaf 1 -out pop1 -fai fai.fai -issim 1")
       system("../angsd -glf pop2.glf.gz -nind 8 -doSaf 1 -out pop2 -fai fai.fai -issim 1")
       system("../misc/realSFS pop1.saf.idx >pop1.saf.idx.ml")
       system("../misc/realSFS pop2.saf.idx >pop2.saf.idx.ml")
       system("../misc/realSFS pop1.saf.idx pop2.saf.idx >pop1.pop2.saf.idx.ml")
   }
   if(FALSE){
       pop1 <- exp(scan("pop1.saf.idx.ml"))
       pop2 <- exp(scan("pop2.saf.idx.ml"))
       pop1.pop2 <- matrix(exp(scan("pop1.pop2.saf.idx.ml")),nPop1+1,byrow=T)
       par(mfrow=c(1,2))
       barplot(rbind(norm(table(p1.d)),pop1),be=T,main="only varsites pop1")
       barplot(rbind(norm(table(p2.d)),pop2),be=T,main="only varsites pop2")
       range(norm(sfs.2d)-t(pop1.pop2))
       ##[1] -0.0005150658  0.0004685074

       barplot(rbind(rowSums(norm(t(sfs.2d))),rowSums(pop1.pop2)),be=T)
       barplot(rbind(colSums(norm(t(sfs.2d))),colSums(pop1.pop2)),be=T)

   }
   if(FALSE){
       ##simulate angsd inputfiles with invariable sites and run it
       system("../misc/msToGlf -in msoutput.txt -out raw -singleOut 1 -regLen 10000000 -depth 8 -err 0.005")
       system("../misc/splitgl raw.glf.gz 20 1 12 >pop1.glf.gz")
       system("../misc/splitgl raw.glf.gz 20 13 20 >pop2.glf.gz")
       system("echo \"1 250000000\" >fai.fai")
       system("../angsd -glf pop1.glf.gz -nind 12 -doSaf 1 -out pop1 -fai fai.fai -issim 1")
       system("../angsd -glf pop2.glf.gz -nind 8 -doSaf 1 -out pop2 -fai fai.fai -issim 1")
       system("../misc/realSFS pop1.saf.idx >pop1.saf.idx.ml")
       system("../misc/realSFS pop2.saf.idx >pop2.saf.idx.ml")
       system("../misc/realSFS pop1.saf.idx pop2.saf.idx >pop1.pop2.saf.idx.ml")

   }
   if(FALSE){
       pop1 <- norm(exp(scan("pop1.saf.idx.ml"))[-1])
       pop2 <- norm(exp(scan("pop2.saf.idx.ml"))[-1])
       pop1.pop2 <- matrix(exp(scan("pop1.pop2.saf.idx.ml")),nPop1+1,byrow=T)
       par(mfrow=c(1,2))
       barplot(rbind(norm(table(p1.d)[-1]),pop1),be=T,main="varsites pop1")
       barplot(rbind(norm(table(p2.d)[-1]),pop2),be=T,main="varsites pop2")
       pop1.pop2[1,1] <- 0
       pop1.pop2[nrow(pop1.pop2),ncol(pop1.pop2)] <- 0
       pop1.pop2 <- norm(pop1.pop2)
       range(norm(sfs.2d)-t(pop1.pop2))
#[1] -0.0005047007  0.0007018686
 
       barplot(rbind(rowSums(norm(t(sfs.2d))),rowSums(pop1.pop2)),be=T)
       barplot(rbind(colSums(norm(t(sfs.2d))),colSums(pop1.pop2)),be=T)

   }
   if(FALSE){
       ##just redo the angsd and optimization
       ##git checkout master ;make clean;make
       system("../angsd -glf pop1.glf.gz -nind 12 -doSaf 1 -out pop1 -fai fai.fai -issim 1 -P 10")
       system("../angsd -glf pop2.glf.gz -nind 8 -doSaf 1 -out pop2 -fai fai.fai -issim 1 -P 10")
       system("../misc/realSFS pop1.saf 24 -P 60 >pop1.saf.idx.ml")
       system("../misc/realSFS pop2.saf 16 -P 60 >pop2.saf.idx.ml")
       system("../misc/realSFS 2dsfs pop1.saf pop2.saf 24 16 -P 60 >pop1.pop2.saf.idx.ml")
   }
   if(FALSE){
       pop1 <- norm(exp(scan("pop1.saf.idx.ml"))[-1])
       pop2 <- norm(exp(scan("pop2.saf.idx.ml"))[-1])
       pop1.pop2 <- matrix(exp(scan("pop1.pop2.saf.idx.ml")),nPop1+1,byrow=T)
       par(mfrow=c(1,2))
       barplot(rbind(norm(table(p1.d)[-1]),pop1),be=T,main="varsites pop1")
       barplot(rbind(norm(table(p2.d)[-1]),pop2),be=T,main="varsites pop2")
       pop1.pop2[1,1] <- 0
       pop1.pop2[nrow(pop1.pop2),ncol(pop1.pop2)] <- 0
       pop1.pop2 <- norm(pop1.pop2)
       range(norm(sfs.2d)-t(pop1.pop2))
       ##       [1] -0.0005046856  0.0007019217

   }
   
}


</pre>