First of all, I hope this email finds you well! I am trying to implement smc++ and I am using 1000 Genomes Project data as a test. I am using mappability bed files from https://share.eva.mpg.de/index.php/s/ygfMbzwxneoTPZj, and I've been playing a bit with some parameters.
I am using all samples from YRI and CEU populations and my command is:
smc++ estimate --outdir analysis_test/ --timepoints 1 350000 --spline cubic --base YRI.cubic.timepoints.allsamples --cores 8 1.25e-8 out_test/YRI.WGS.allsamples.chr*.smc.gz
and my plotting command is:
smc++ plot YRI.CEU.cubic.timepoints.allsamples.final.png -c -g 30 --cores 5 analysis_test/YRI.cubic.timepoints.allsamples.final.json analysis_test/CEU.cubic.timepoints.allsamples.final.json
I've been getting Ne trajectories that do make sense for these populations, but the scaling on the x-axis is quite off. The program is placing the out-of-Africa bootleneck at 10^2 years ago and it happened ~50-80k years ago. I've been trying to change some parameters and I am still getting plots similar to the one below. Do you have any suggestions as to why the timing could be off? I would really appreciate some help here. Thanks a lot in advance.
Hi,
First of all, I hope this email finds you well! I am trying to implement smc++ and I am using 1000 Genomes Project data as a test. I am using mappability bed files from https://share.eva.mpg.de/index.php/s/ygfMbzwxneoTPZj, and I've been playing a bit with some parameters.
I am using all samples from YRI and CEU populations and my command is:
smc++ estimate --outdir analysis_test/ --timepoints 1 350000 --spline cubic --base YRI.cubic.timepoints.allsamples --cores 8 1.25e-8 out_test/YRI.WGS.allsamples.chr*.smc.gzand my plotting command is:smc++ plot YRI.CEU.cubic.timepoints.allsamples.final.png -c -g 30 --cores 5 analysis_test/YRI.cubic.timepoints.allsamples.final.json analysis_test/CEU.cubic.timepoints.allsamples.final.jsonI've been getting Ne trajectories that do make sense for these populations, but the scaling on the x-axis is quite off. The program is placing the out-of-Africa bootleneck at 10^2 years ago and it happened ~50-80k years ago. I've been trying to change some parameters and I am still getting plots similar to the one below. Do you have any suggestions as to why the timing could be off? I would really appreciate some help here. Thanks a lot in advance.