Empty Eigenstrat data after merging
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8 months ago
hodiv99219 • 0

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 ?

eigenstrat admixR aDNA population genetics • 297 views
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