plink snp select
plink --file data --recodeAD --recode-allele recode.txt ..... to select all SNPs within this 5000kb region on chromosome 2 (when using --from-kb ..., Plink 1.x normally sets the major allele to A2, and the minor allele to A1. It isn't really possible to do better with .ped + .map filesets which don't ...,Note that this is slightly different from PLINK 1.07's behavior when the main input .... Similarly, --exclude-snp specifies a single variant to exclude; this can also be .... (so it's dangerous to choose a threshold that filters out too many varia, Hi because you are using wrong input file, keep command ponly works on ped and map files, if you have only binary files (bed, bim, fam), use ..., PLINK will generate a number of standard summary statistics that are useful ..... By default, we currently just select exactly two flanking SNPs.,跳到 Extracting a SNP of interest - (to select a region, use the --to and --from options instead, or use --window 100 with --snp to select a 100kb region ... , If you're fine with the main body of the file containing allele counts (0/1/2) rather than allele names, you can use. plink --bfile data --extract ..., --file, plink}, Specify .ped and .map files ... --snps, SNP list}, Select comma-delimited list of SNPs, allowing for ranges, e.g. snp1,snp2,snp6- ..., Not sure of having understood your issue, but the .bim file describes the extended variant information, one variant per line. You have not ...,#1 is correct. However, you don't need to code your own SNP selection logic; PLINK's --indep-pairwise command does this for you. Try something like
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 plink snp select 相關參考資料
Extract SNPs - PLINK: Whole genome data analysis toolset
plink --file data --recodeAD --recode-allele recode.txt ..... to select all SNPs within this 5000kb region on chromosome 2 (when using --from-kb ... http://zzz.bwh.harvard.edu How does Plink choose which SNP is Allele1 and Allele2? - Biostars
Plink 1.x normally sets the major allele to A2, and the minor allele to A1. It isn't really possible to do better with .ped + .map filesets which don't ... https://www.biostars.org Input filtering - PLINK 1.9 - cog-genomics.org
Note that this is slightly different from PLINK 1.07's behavior when the main input .... Similarly, --exclude-snp specifies a single variant to exclude; this can also be .... (so it's dangerou... https://www.cog-genomics.org Keep A Subset Of Samples In Plink - Biostars
Hi because you are using wrong input file, keep command ponly works on ped and map files, if you have only binary files (bed, bim, fam), use ... https://www.biostars.org PLINK
PLINK will generate a number of standard summary statistics that are useful ..... By default, we currently just select exactly two flanking SNPs. http://zzz.bwh.harvard.edu PLINK tutorial - PLINK: Whole genome data analysis toolset
跳到 Extracting a SNP of interest - (to select a region, use the --to and --from options instead, or use --window 100 with --snp to select a 100kb region ... http://zzz.bwh.harvard.edu Plink: Retrieving specific SNP data for individuals in dataset ...
If you're fine with the main body of the file containing allele counts (0/1/2) rather than allele names, you can use. plink --bfile data --extract ... https://www.biostars.org Reference - PLINK: Whole genome data analysis toolset
--file, plink}, Specify .ped and .map files ... --snps, SNP list}, Select comma-delimited list of SNPs, allowing for ranges, e.g. snp1,snp2,snp6- ... http://zzz.bwh.harvard.edu Retrieve a subset of SNPs in Plink - Biostars
Not sure of having understood your issue, but the .bim file describes the extended variant information, one variant per line. You have not ... https://www.biostars.org Tagging SNPs in PLINK - Biostars
#1 is correct. However, you don't need to code your own SNP selection logic; PLINK's --indep-pairwise command does this for you. Try something like https://www.biostars.org |