Warning while using mergeit

[ShreyaAdhya]

Hi,

using the mergeit tool, I'm getting the following output :

---

parameter file: merge1.txt
geno1: pop1.geno
snp1: pop1.snp
ind1: pop1.ind
geno2: pop2.geno
snp2: pop2.snp
ind2: pop2.ind
outputformat: EIGENSTRAT
genooutfilename: merged_files/merged.geno
snpoutfilename: merged_files/merged.snp
indoutfilename: merged_files/merged.ind
allele funny: rs3866853 C T C A
allele funny: rs186227113 T C T G
allele funny: rs76848438 G T T C
allele funny: rs571647631 T C T G
allele funny: rs536650371 C T C A
allele funny: rs569883333 G A G T
allele funny: rs533376218 A G A C
allele funny: rs12922580 T G T C
allele funny: rs540831825 A C A G
allele funny: rs536259035 G A G T
allele funny: rs7246683 T G G A
numsnps input: 22080043 38851429
eigenstrat output
numsnps output: 10100139 numindivs: 1164

Histogram of checkmatch return codes
kode: -1 2 X allele and strandcheck
kode: -2 1808577 A/T or C/G and strandcheck
kode: 0 11 Allele mismatch
kode: 1 9135811 SNP OK (no flip)
kode: 2 964328 SNP OK (flip)
total: 11908729

Over here,
--> what is exactly meant by 'allele funny' giving allele mismatch?
--> is the number of SNPs in the input files dropping from 20M and 30M to 10M in the output file, fine?

Thanks in advance!

you can try and manually delete the mismatched snps ,, it worked for me actually

[bumblenick]

allele funny means that the allele values in your 2 files are inconsistent such as "T C" and "T G" Such alleles are dropped in the output. But this can be a symptom of deeper problems and you should for example run a PCA and make sure that it looks OK \\ Nick

…

On Fri, Feb 17, 2023 at 1:30 AM ShreyaAdhya ***@***.***> wrote: Hi, using the mergeit tool, I'm getting the following output : ------------------------------ parameter file: merge1.txt geno1: pop1.geno snp1: pop1.snp ind1: pop1.ind geno2: pop2.geno snp2: pop2.snp ind2: pop2.ind outputformat: EIGENSTRAT genooutfilename: merged_files/merged.geno snpoutfilename: merged_files/merged.snp indoutfilename: merged_files/merged.ind allele funny: rs3866853 C T C A allele funny: rs186227113 T C T G allele funny: rs76848438 G T T C allele funny: rs571647631 T C T G allele funny: rs536650371 C T C A allele funny: rs569883333 G A G T allele funny: rs533376218 A G A C allele funny: rs12922580 T G T C allele funny: rs540831825 A C A G allele funny: rs536259035 G A G T allele funny: rs7246683 T G G A numsnps input: 22080043 38851429 eigenstrat output numsnps output: 10100139 numindivs: 1164 Histogram of checkmatch return codes kode: -1 2 X allele and strandcheck kode: -2 1808577 A/T or C/G and strandcheck kode: 0 11 Allele mismatch kode: 1 9135811 SNP OK (no flip) kode: 2 964328 SNP OK (flip) total: 11908729 Over here, --> what is exactly meant by 'allele funny' giving allele mismatch? --> is the number of SNPs in the input files dropping from 20M and 30M to 10M in the output file, fine? Thanks in advance! — Reply to this email directly, view it on GitHub <#100>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77BZQCAM4BKOBV6XYCM3WX4LJ5ANCNFSM6AAAAAAU7BWXA4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>