when merge two file with plink1.9, many warning about two variants have the same postion.

[MAOMAO]

Hi All,

I am trying to merge two .ped .map files, however,  it has lots of warning: two variants have the same position (highlighted in red). I have no idea what's wrong with this? Any suggestion would be appreciated.

plink1.9 --file merged --merge Plate_3_Plink --recode --out merged1
PLINK v1.90b3.45 64-bit (13 Jan 2017) https://www.cog-genomics.org/plink2(C) 2005-2017 Shaun Purcell, Christopher Chang GNU General Public License v3Logging to merged1.log.Options in effect: --file merged --merge Plate_3_Plink --out merged1 --recode7483 MB RAM detected; reserving 3741 MB for main workspace..ped scan complete (for binary autoconversion).Performing single-pass .bed write (1914935 variants, 120 people).--file: merged1-temporary.bed + merged1-temporary.bim + merged1-temporary.famwritten.120 people loaded from merged1-temporary.fam.95 people to be merged from Plate_3_Plink.ped.Of these, 95 are new, while 0 are present in the base dataset.1914935 markers loaded from merged1-temporary.bim.1914935 markers to be merged from Plate_3_Plink.map.Of these, 0 are new, while 1914935 are present in the base dataset.Warning: Variants 'ilmnseq_rs9701872_ilmndup1' and 'ilmnseq_rs9701872' have thesame position.Warning: Variants 'exm2268640' and 'JHU_1.762319' have the same position.Warning: Variants 'rs35660652' and 'JHU_1.821925' have the same position.83384 more same-position warnings: see log file.Performing single-pass merge (215 people, 1914935 variants).Merged fileset written to merged1.bed + merged1.bim + merged1.fam .1914935 variants loaded from .bim file.215 people (0 males, 213 females, 2 ambiguous) loaded from .fam.Ambiguous sex IDs written to merged1.nosex .Using 1 thread (no multithreaded calculations invoked).Before main variant filters, 215 founders and 0 nonfounders present.Calculating allele frequencies... done.Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commandstreat these as missing.Total genotyping rate is 0.989421.1914935 variants and 215 people pass filters and QC.Note: No phenotypes present.--recode ped to merged1.ped + merged1.map ... done.

[Christopher Chang]

You should know whether or not same-position variants are expected.  If they're expected, you can safely ignore the warning.

In the meantime, please figure out a better way to post .log transcripts; omitting linebreaks is absurd.

[Ying Zhao]

Hi Christopher,

Thanks for your reply. I will figure out a better way to post .log transcripts. 

For the same position variants, I check they have the same alleles and on the same chr. There are over 83000 same-position warnings, your mentioned that I should know whether or not same position variants are expected, does that mean that it totally depends on my further analysis? 

Thanks,

MAOMAO

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