I tried running Dsuite on a vcf file containing approx 9.65 million variants using both Dtrios and Dparallel . Though the final excecution has been completed but there are discrepancies with the results. (Note - I have taken 5 population including the outgroup specified).
1. Though i didnt give the flag ( --no-f4-ratio ) still the f4 ratio hasnt been computed and the output is showing 0 for both runs of the same vcf file using Dtrios and Dparallel.
For Dtrios I ran the command -[./Build/Dsuite Dtrios merged_chr1.vcf SETS.txt] and obtained the given output-
For DParallel I ran the command -[./utils/DtriosParallel SETS.txt merged_chr1.vcf] and obtained the given output-
There is a significant difference in the Z-score and P-value in the results from Dtrios and DParallel though the same vcf file and sets.txt file (5 populations including outgroup specified) have been used . Please check the output Dtrios and DParallel file attached above and kindly explain these discrepancies.
I tried running Dsuite on a vcf file containing approx 9.65 million variants using both Dtrios and Dparallel . Though the final excecution has been completed but there are discrepancies with the results. (Note - I have taken 5 population including the outgroup specified). 1. Though i didnt give the flag ( --no-f4-ratio ) still the f4 ratio hasnt been computed and the output is showing 0 for both runs of the same vcf file using Dtrios and Dparallel. For Dtrios I ran the command -[./Build/Dsuite Dtrios merged_chr1.vcf SETS.txt] and obtained the given output-
For DParallel I ran the command -[./utils/DtriosParallel SETS.txt merged_chr1.vcf] and obtained the given output-
