Question: Bmerge Files In Plink
1
gravatar for Zhshqzyc
2.7 years ago by
Zhshqzyc320
Zhshqzyc320 wrote:

Hello,

I have 23 chromsome binary files (.bim .fam .bed), is there a plink command merge them together? Suppose they are in different folders such as 1,2,3....23

Thanks

ADD COMMENTlink written 2.7 years ago by Zhshqzyc320
0
gravatar for Keith James
2.7 years ago by
Keith James5.4k
UK
Keith James5.4k wrote:

plink --noweb --make-bed --bfile [?] --merge-list list.txt --out [?]

[?]first basename[?] is the base name (i.e. WITHOUT the .bed, .bim or .fam suffix) of one of the chromosomes' file sets, while list.txt contains the filenames of the other chromosomes' file sets (i.e. all except the one given on the command line), but this time WITH the .bed, .bim or .fam suffix

second.bed second.bim.second.fam
third.bed third.bim.third.fam

You can use paths in this file i.e. /path/to/second.bed etc. I don't know if the order of the files on each line matters.

Plink may be very useful, but its command line interface can be confusing.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Keith James5.4k

I used the binary files. Can you look at this: Analysis started: Mon Jul 25 14:12:09 2011

Options in effect: --make-bed --bfile --merge-list allfiles.txt --out

ERROR: No file [ --merge-list.fam ] exists. Press any key to continue . . .

ADD REPLYlink written 2.7 years ago by Zhshqzyc320

Ignore it.

PLINK --bfile basefile --merge-list allfiles.txt --make-bed --out

Detected that binary PED file is v1.00 SNP-major mode WARNING DUPLICATE MARKERS FOUND *** Duplicate marker name found: [ rs1051740 ] Duplicate marker name found: [ rs10924425 ]

Using merge mode 1 : consensus call (default) Problem encountered merging files, with the following markers: rs1051740 rs10924425 [ dump info: sizes = 415906 and 415908 ]

ERROR: Cannot merge files. Check your MAP files. Press any key to continue . . .

ADD REPLYlink written 2.7 years ago by Zhshqzyc320

Ignore it.

My command

PLINK --bfile basefile --merge-list allfiles.txt --make-bed --out

Detected that binary PED file is v1.00 SNP-major mode WARNING DUPLICATE MARKERS FOUND *** Duplicate marker name found: [ rs1051740 ] Duplicate marker name found: [ rs10924425 ]

Using merge mode 1 : consensus call (default) Problem encountered merging files, with the following markers: rs1051740 rs10924425 [ dump info: sizes = 415906 and 415908 ]

ERROR: Cannot merge files. Check your MAP files. Press any key to continue . . .

ADD REPLYlink written 2.7 years ago by Zhshqzyc320

[code]Ignore it. My command PLINK --bfile basefile --merge-list allfiles.txt --make-bed --out Detected that binary PED file is v1.00 SNP-major mode * WARNING DUPLICATE MARKERS FOUND ** Duplicate marker name found: [ rs1051740 ] Duplicate marker name found: [ rs10924425 ] Using merge mode 1 : consensus call (default) Problem encountered merging files, with the following markers: rs1051740 rs10924425 [ dump info: sizes = 415906 and 415908 ] ERROR: Cannot merge files. Check your MAP files. Press any key to continue . . . –[/code]

ADD REPLYlink written 2.7 years ago by Zhshqzyc320

Plink is trying to merge the files, but it is finding that some SNPs are duplicated. You should check your inputs to find out why.

ADD REPLYlink written 2.7 years ago by Keith James5.4k
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