lgen to ped using plink

Question

[tarek.mohamed]

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.

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

Answer 1

[chrchang523]

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.

[tarek.mohamed]

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.

Tarek