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
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 + test_1_1.9.map ... done.