Warning: different physical position for rs365066

Question

[dirranrak]

Hello,

I had this error when I tried to merge two binary files with plink 1.07.

Warning: different physical position for rs3926405
Warning: different physical position for rs365066

Found 58757 SNPs that do not match in terms of allele codes
Might include strand flips, although flipped A/T and C/G SNPs will be undetected)
Writing problem SNPs to [ AfricaKhoisangeno0.05hwe0.001Batwakiga.missnp ]

ERROR: Stopping due to mis-matching SNPs -- check +/- strand?

So I excluded these two SNPs in the first file and I followed this tip:

plink --bfile source2 --flip merged.missnp --make-bed --out source2_trial
plink --bfile source1 --bmerge source2_trial --make-bed --out merged_trial
plink --bfile source2_trial --flip merged_trial.missnp --make-bed --out source2_corrected

and it worked but in the case that there is many more error about SNPs physical position, what should I do? I do not want to loose too many SNPs data as I did before.

Thank you

[dirranrak]

Hi Philipp, Thank you for the advice, it was usefull.

Answer 1

[Philipp Bayer]

This normally happens when your source files are from different chromosomal builds - for example for rs3926405, dbSNP reports two positions, one at 105946839 on chromosome 2 in GRCCh38, one at 106563295 on chromosome 2 in GRCh37. Could you check and verify whether your two source have these two positions?

For example, do

grep rs3926405 your_first_map_file your_second_map_file

If it turns out to have these two positions, then I recommend to use any lift-over tool, here's an overview: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)

Answer 2

[dirranrak]

Hi all,

I advanced using ADMIXTURE and I have got K=5, so I ploted the data with R using col=5. I get the barplot with each bar representing an individual but how can I recognize the color label? because the *.5.Q data doesn't have either row or column title header but just the proportions for each individual.

Thank you