plink snp select
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
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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 |