szpiech
commented
2 months ago Hi James,
Hmm, well the search space for the A parameter has a weird relationship to the minimum observed distance between two snps in the data set, so this is probably fine. The lambda values aren't really comparable between species or even populations, so 90 is also probably fine for your data (I've seen this approx max value for some ape data with small sample sizes).
-Zachary
On Sun, May 12, 2024 at 6:29 PM James Santangelo @.***> wrote:
Hello,
I've run lassi using the following command separately for each of 16 chromosomes:
lassip --vcf {{chrom}}_phased.vcf.gz --hapstats --calc-spec --salti --winsize 201 --winstep 100 --threads 2 --pop popfile.txt --out {{chrom}}_test
I then ran the following command to estimate m, A, and L across all 16 chromosomes:
lassip --spectra *.lassip.hap.spectra.gz --salti --out test --map allChroms.map --threads 2 --k 20 --dist-type cm
I've noticed the values of A I'm getting are really low compared to those reported in the manuscript, such that if I take the log of these values they're all negative. Is this expected behavior? The values of Lambda I'm getting are also quite low (the max is ~90) compared to published values.
image.png (view on web) https://github.com/szpiech/lassip/assets/26078946/ebe3a943-dd94-4366-9e0c-da6ced381d06
Thanks! James
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Hello,
I've run lassi using the following command separately for each of 16 chromosomes:
lassip --vcf {{chrom}}_phased.vcf.gz --hapstats --calc-spec --salti --winsize 201 --winstep 100 --threads 2 --pop popfile.txt --out {{chrom}}_testI then ran the following command to estimate m, A, and L across all 16 chromosomes:
lassip --spectra *.lassip.hap.spectra.gz --salti --out test --map allChroms.map --threads 2 --k 20 --dist-type cmI've noticed the values of A I'm getting are really low compared to those reported in the manuscript, such that if I take the log of these values they're all negative. Is this expected behavior? The values of Lambda I'm getting are also quite low (the max is ~90) compared to published values.
Thanks! James