Hi, just wanted some clarification on kept vs discarded sites. I understand the default is to discard monomorphic sites. However, the number of discarded sites appears to increase as SweeD runs through all the alignments in my datasets (vcf of scaffolds, not chromosomal level), and the number of kept sites is negative. I have not found any discussion on this issue, and I'm not sure whether to trust the results I am getting, as I suspect a parsing issue reading the vcf?
Hi, just wanted some clarification on kept vs discarded sites. I understand the default is to discard monomorphic sites. However, the number of discarded sites appears to increase as SweeD runs through all the alignments in my datasets (vcf of scaffolds, not chromosomal level), and the number of kept sites is negative. I have not found any discussion on this issue, and I'm not sure whether to trust the results I am getting, as I suspect a parsing issue reading the vcf?
SweeD_Info.AE_Norway_test.txt
Command: ./SweeD -name AE_Norway_test -input Norway_sub.recode.vcf -folded -grid 100