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!

[DevYansh-net]

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: ***@***.***>