ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.918/0.919 on github), see Change_log for changes, and download it here.

ThetaStat

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Small program to do window statistics.

Here is what the program is supposed to do.

1) define a positionstart pS, as from the first position(on the genome) with data.
2) find a positionstep pE, which is pS+winsize. If pE is after the last position(on the genome) with data exit.
3) calculate statistics using the region that is spanned by pS and pE.
4) increment pS with stepsize, goto step 2). 


./thetaStat
	'./thetaStat': a program to do neutrality test statistics using thetas.idx output from angsd

	Examples:
	1) ./thetaStat print angsdput.thetas.idx
	2) ./thetaStat do_stat angsdput.thetas.idx -win 5000 -step 1000

	Type './thetaStat do_stat' or './thetaStat print' for more information
./thetaStat print

	./thetaStat print angsdput.thetas.idx [-r chrName]

	Examples:
	1)./thetaStat print angsdput.thetas.idx
	2)./thetaStat print angsdput.thetas.idx -r chr2
./thetaStat do_stat

	./thetaStat do_stat .thetas.idx [-win INT -step INT -r chrName -type [0,1,2] -outnames outputprefix]

	Examples:
	1)./thetaStat do_stat angsdput.thetas.idx
	2)./thetaStat do_stat angsdput.thetas.idx -win 5000 -step 1000
	3)./thetaStat do_stat angsdput.thetas.idx -win 5000 -step 1000 -r chr1
	4)./thetaStat do_stat angsdput.thetas.idx -win 5000 -step 1000 -r chr1 -nChr 20 -outnames newoutputname