Question: illumina genotype reports _lgen to ped using plink
0
gravatar for tarek.mohamed
10 weeks ago by
tarek.mohamed110
tarek.mohamed110 wrote:

Hi All,

I have an illumina genotype final report, and I want to convert it to .ped using plink. I prepared three files; fam, lgen, and fam (please find below a snap shot for these files ) Then I used plink, but O got the error Variant 'rs1000002' in .lgen file has 3+ different alleles. Although, as you can see from the first line of lgen file, Variant 'rs1000002' has only two alleles

$ plink -lfile 200638550003_R01C01 --no-parents --no-sex --no-pheno --recode

PLINK v1.90b3.32 64-bit (24 Feb 2016) https://www.cog-genomics.org/plink2 (C) 2005-2016 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to plink.log. Options in effect: --lfile 200638550003_R01C01 --no-parents --no-pheno --no-sex --recode

128715 MB RAM detected; reserving 64357 MB for main workspace. Processing .lgen file... 0%Error: Variant 'rs1000002' in .lgen file has 3+ different alleles.

lgen_file:

200638550003_R01C01 NA1 rs1000002 A G

200638550003_R01C01 NA2 rs1000003 A G

200638550003_R01C01 NA3 rs10000030 A G

fam_file: 200638550003_R01C01 NA1 0 0 0 0

200638550003_R01C01 NA2 0 0 0 0

200638550003_R01C01 NA3 0 0 0 0

map_file: 3 rs1000002 0 183635768

3 rs1000003 0 98342907

4 rs10000030 0 103374154

ADD COMMENTlink modified 10 weeks ago by chrchang5232.8k • written 10 weeks ago by tarek.mohamed110
0
gravatar for chrchang523
10 weeks ago by
chrchang5232.8k
United States
chrchang5232.8k wrote:

That build had a .lgen loading bug which was fixed the following month; retry with a newer plink 1.9 build.

ADD COMMENTlink written 10 weeks ago by chrchang5232.8k

can you send me the link for this newer build. Also, can I do this with plink2? I searched plink2 but I could not --file flag Thanks

ADD REPLYlink written 10 weeks ago by tarek.mohamed110

This is downloadable from https://www.cog-genomics.org/plink/1.9/ .

(As for why plink 2.0 doesn't have the --file flag yet, that's lower priority because plink 1.9 already has a good implementation. The first development priority is enabling important things that can't be done at all with plink 1.9.)

ADD REPLYlink written 10 weeks ago by chrchang5232.8k

Hi Christopher, 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.

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

fam_file: 200638550003_R01C01 200638550003_R01C01 0 0 0 0

map_file

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

log_file:

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 + test_1_1.9.map ... done.

Thanks Tarek

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

Well, it doesn't look like you posted the entire .lgen or .map files (only 4 variants, when the .log clearly indicates there were 10), so there's no way to tell if they match.

Note that the .map file you did post has out-of-order variants, and plink automatically sorts them by position before generating the new .ped + .map fileset.

ADD REPLYlink written 10 weeks ago by chrchang5232.8k
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