jianzeng
commented
1 year ago Hi,
This error means this SNP has minor allele frequency (MAF) = 0, so it cannot compute the LD with other SNPs. Please filter SNPs based on their MAF first using Plink, e.g.
Plink --bfile myplink_wt22 --maf 0.01 --make-bed --out qced
If you don’t want to generate a new bed file, you can use --write-snplist instead of –make-bed in the above command.
Thanks, JZ
From: amanouchehrinia @.> Reply to: jianyangqt/gcta @.> Date: Friday, 12 May 2023 at 8:28 am To: jianyangqt/gcta @.> Cc: Subscribed @.> Subject: [jianyangqt/gcta] Error: rs... is a fixed SNP! (Issue #40)
Hi Everyone, Googled for a while to find a solution for this error but cannot find any help. Was wondering if anyone has a solution or a tip. The program works fine on the provided 1000G file. Here is the summary:
- GCTB 2.05beta *
- Genome-wide Complex Trait Bayesian analysis *
- Authors: Jian Zeng, Luke Lloyd-Jones, Zhili Zheng, Shouye Liu *
- MIT License *
Analysis started: Fri May 12 00:22:23 2023
Options:
--bfile myplink_22 --make-full-ldm --out test_chr22
Reading PLINK FAM file from [myplink_22.fam]. 1050 individuals to be included from [myplink_22.fam]. Reading phenotypes from [myplink_22.fam]. Non-missing phenotypes of trait 1 of 1050 individuals are included from [myplink_22.fam]. 1050 matched individuals are kept. Reading PLINK BIM file from [myplink_22.bim]. 110260 SNPs to be included from [myplink_22.bim]. 110260 SNPs on 1 chromosomes are included. Building full LD matrix for all SNPs ... Reading PLINK BED file from [myplink_22.bed] in SNP-major format ...
Error: rs188716078 is a fixed SNP!
Analysis finished: Fri May 12 00:22:24 2023 Computational time: 0:0:1
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Hi Everyone, Googled for a while to find a solution for this error but cannot find any help. Was wondering if anyone has a solution or a tip. The program works fine on the provided 1000G file. Here is the summary:
Analysis started: Fri May 12 00:22:23 2023
Options:
--bfile myplink_22 --make-full-ldm --out test_chr22
Reading PLINK FAM file from [myplink_22.fam]. 1050 individuals to be included from [myplink_22.fam]. Reading phenotypes from [myplink_22.fam]. Non-missing phenotypes of trait 1 of 1050 individuals are included from [myplink_22.fam]. 1050 matched individuals are kept. Reading PLINK BIM file from [myplink_22.bim]. 110260 SNPs to be included from [myplink_22.bim]. 110260 SNPs on 1 chromosomes are included. Building full LD matrix for all SNPs ... Reading PLINK BED file from [myplink_22.bed] in SNP-major format ...
Error: rs188716078 is a fixed SNP!
Analysis finished: Fri May 12 00:22:24 2023 Computational time: 0:0:1