Hi, Sorry for the beginner question but I did map my dataset (8 individuals modern and ancient DNA) to hs37d5 and did the pseudohaploid call on all sites; I end up with eigenstrat output with the .snp having 38M snps. After that I wanted to merge my dataset with the 1240K eigenstrat dataset, i do so using the build in "mergeit" function from the package.
However while I merge the two dataset I have this error displaying:
Local.snp: genetic distance set from physical distance
On top of that, the .geno and .snp file are empty, while the .ind were merged successfully.
I guessed it was because I don't use the same reference as they do ?
The pipeline I used worked on previous dataset, the only stuff that changed is that I don't specify SNPs to do the calling (i also noticed that the output is myoutput.snp.txt instead of myoutput.snp usually.. but after renaming it, everything is fine on that end)
I also thought it was due that my dataset wasn't in Eigenstrat format but I did specified my calling as follow:
samtools mpileup -R -B -q 1 -f hs37d5.fa -b BAMLIST.txt | awk '$3=="R" {$3="N"; print} {print}' | pileupCaller --sampleNameFile SAMPLELIST.txt --samplePopName TESTOUT -o EigenStrat -e Call/Local
Does anyone have an idea why can't i merge those two datasets ?
