search

esrud / GONE

GONE: Scripts, programs and an example data set
42 stars 3 forks source link

The OUTPUT file show only 9 chr and result a litle bit weird. #37

Open nat6an opened 6 months ago

nat6an commented 6 months ago

Hello Armando

I ran GONe with five groups, three samples per each group (19 chr).

CHMM : ~3 M SNPs KY : ~ 9 M SNPs Mid-south : ~ 11 M SNPs Southernmost : ~11 M SNPs Western : ~ 8 M SNPs

I aware that the SNPs it was not along with the recommened maximum number. However, I got the result.

I look into the OUTPUT* file, CHMM, KY and Southernmost population, show ran all chromosome (19). But Mid-south and Western ran only 9 chromosome (the OUTPUT* show only 9 chr)

5pop_generation 5pop_year

At first, I think it may effect by high number of SNPs. I reduce the SNP (plink to randomly select a subset of SNPs) as you recommend. I test with Western population, 5 M SNPs and every chromosome less than 1M (max is chr 1 with 472,701)

But the the OUTPUT_* file still show only 9 chromosome like this

...... CHROMOSOME 9 NIND(real sample)=3 NSNP=49887 NSNPcalculations=13073 NSNP+2alleles=36206 NSNP_zeroes=0 NSNP_monomorphic=608 NIND_corrected=3.000000 freq_MAF=0.166667 F_dev_HW (sample)=0.368993 F_dev_HW (pop)=0.529888 No genetic distances; using 1.000000 cM per Mb

INPUT FOR GONE

2 Phase (0: pseudohaploids; 1: known phase; 2: unknown phase) 3.000000 sample size (individuals; corrected for zeroes) 0.372837 Hardy-Weinberg deviation 358290665 0.347884 0.945694 2 .......

armando-caballero commented 6 months ago

Not sure why, but with just 3 individuals I do not think any analysis will be reliable at all. Best wishes, Armando