Open slcapel opened 9 months ago
I actually figured this out - the .saf.idx file was also unsorted because I multithreaded (-P 24). When I run on just one thread the files remain sorted. I'm wondering if it's possible to adjust how the realSFS utility multithreads so that files will remain sorted.
Hello, I'm trying to calculate theta values using sliding window means and there is an issue with the
.thetas.idx
file fromrealSFS saf2theta
. All SNPs have theta values calculated, but for some reason most, but not all, of the SNPs for each scaffold are out of order, causing thefirstpos
andlastpos
values to be incorrect. I'm using the bioconda install of version 0.940 and my VCF is made up of hard calls generated using GATK4. Here's the code I used to generate the theta output files:This is what the out.thetas.idx scaffold information looks like:
Due to the SNPs being out of order, when I try to run
thetaStat do_stat out.thetas.idx -win 5000 -step 1000
I get:I'm not sure if this is something I'm doing incorrectly on my end or if it's a slight bug in generating the .thetas.idx file. Please let me know if you need any other information.