Question: lgen to ped using plink
gravatar for tarek.mohamed
10 weeks ago by
tarek.mohamed110 wrote:

Hi All, How can I create a lgen file which has only one individual genotyped for 300,000 SNPs. I mean in the context of sample ids, what shall I use? I created the lgen, fam files below. Then I used plink 1.9 to generate ped file (log file shown belos). The problem is that genotypes in ped file mismatch genotype in lgen file.


200638550003_R01C01 200638550003_R01C01 rs1000002 A G

200638550003_R01C01 200638550003_R01C01 rs1000003 A G

200638550003_R01C01 200638550003_R01C01 rs10000030 A G

200638550003_R01C01 200638550003_R01C01 rs10000037 G G


200638550003_R01C01 200638550003_R01C01 0 0 0 0


3 rs1000002 0 183635768

3 rs1000003 0 98342907

4 rs10000030 0 103374154

4 rs10000037 0 38924330

ped_file: 200638550003_R01C01 200638550003_R01C01 0 0 0 -9 A A G A G A G A G G G A G A A A A A G G


PLINK v1.90b4.6 64-bit (15 Aug 2017) Options in effect: --lfile test_1 --no-fid --no-parents --no-pheno --no-sex --out test_1_1.9 --recode

Hostname: quser11 Working directory: /projects/b1042/BurridgeLab Start time: Wed Sep 13 15:23:58 2017

Random number seed: 1505334238

128715 MB RAM detected; reserving 64357 MB for main workspace.

Processing .lgen file... done.

--lfile: test_1_1.9-temporary.bed + test_1_1.9-temporary.bim +

test_1_1.9-temporary.fam written.

10 variants loaded from .bim file.

1 person (0 males, 0 females, 1 ambiguous) loaded from .fam.

Ambiguous sex ID written to test_1_1.9.nosex .

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 1 founder and 0 nonfounders present.

Calculating allele frequencies... done.

10 variants and 1 person pass filters and QC.

Note: No phenotypes present.

--recode ped to test_1_1.9.ped + ... done.

Thanks Tarek

ADD REPLY • link • edit • moderate modified 11 minutes ago • written 13 minutes ago by tarek.mohamed • 0 Add your answer

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by tarek.mohamed110

Wrote a response earlier, but it seems to have disappeared.

The main issue is that your .map file is unsorted; plink will sort it by position before generating the new .ped + .map fileset, and I'm guessing that's why there appears to be a discrepancy.

Also, it doesn't look like you posted the entire .lgen or .map input files, since they have only 4 variants but the .log file states that 10 were loaded.

ADD REPLYlink written 10 weeks ago by chrchang5232.8k

Hi Chang, Thanks again for the reply. You are right, this discrepancy is due to the unsorted map file. After comparing ped file with a sorted map file, everything seems to be fine now.


ADD REPLYlink written 10 weeks ago by tarek.mohamed110
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