plink prune
Note that this is slightly different from PLINK 1.07's behavior when the main input fileset contains .... --prune filters out all samples with missing phenotypes. , 12plink-1.07/plink --noweb --file input --indep-pairwise 50 5 0.5 --out tmp1plink-1.07/plink --noweb --file input --extract tmp1.prune.in --recode ...,These commands produce a pruned subset of markers that are in approximate linkage equilibrium with each other, writing the IDs to plink.prune.in (and the IDs ... ,If your dataset has a shortage of them, PLINK 1.9 --make-founders may come in handy. ... These commands produce a pruned subset of markers that are in ... , PLINK will generate a number of standard summary statistics that are ..... plink --file data --extract plink.prune.in --make-bed --out pruneddata ..., This is because the .prune.in and .prune.out files contain variant IDs, but your VCF has all variant IDs set to '.' . plink 2.0's --set-all-var-ids flag ..., Variants with a chromosome code of 0 are considered to be unplaced, and are ignored by --indep-pairwise}., It does not seem like an in depth analysis (the link that you posted). If the user feels that clumping is preferable to pruning in every situation, ..., As your intention is to include these variants, you should be extracting variants from the plink.prune.out file. So, 2 possible ways to get what you ...,此步驟會產出兩個檔案：indep.prune.in是獨立的SNPs清單；indep.prune.out是具有LD ... plink --bfile raw-GWA-data --extract indep.prune.in --genome --min 0.1875 ...
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 plink prune 相關參考資料
Input filtering - PLINK 1.9 - cog-genomics.org
Note that this is slightly different from PLINK 1.07's behavior when the main input fileset contains .... --prune filters out all samples with missing phenotypes. https://www.cog-genomics.org LD-prune with plink | lizhong's notes
12plink-1.07/plink --noweb --file input --indep-pairwise 50 5 0.5 --out tmp1plink-1.07/plink --noweb --file input --extract tmp1.prune.in --recode ... https://wlz0726.github.io Linkage disequilibrium - PLINK 1.9 - cog-genomics.org
These commands produce a pruned subset of markers that are in approximate linkage equilibrium with each other, writing the IDs to plink.prune.in (and the IDs ... https://www.cog-genomics.org Linkage disequilibrium - PLINK 2.0 - cog-genomics.org
If your dataset has a shortage of them, PLINK 1.9 --make-founders may come in handy. ... These commands produce a pruned subset of markers that are in ... https://www.cog-genomics.org PLINK
PLINK will generate a number of standard summary statistics that are ..... plink --file data --extract plink.prune.in --make-bed --out pruneddata ... http://zzz.bwh.harvard.edu plink produces does pruning according to log file but prune.in is ...
This is because the .prune.in and .prune.out files contain variant IDs, but your VCF has all variant IDs set to '.' . plink 2.0's --set-all-var-ids flag ... https://www.biostars.org Plink prune.in prune.out blank - Biostars
Variants with a chromosome code of 0 are considered to be unplaced, and are ignored by --indep-pairwise}. https://www.biostars.org Plink: Understanding LD Clumping vs Pruning - BioStar
It does not seem like an in depth analysis (the link that you posted). If the user feels that clumping is preferable to pruning in every situation, ... https://www.biostars.org Using PLINK to filter VCF files - Biostars
As your intention is to include these variants, you should be extracting variants from the plink.prune.out file. So, 2 possible ways to get what you ... https://www.biostars.org 【GWAS】使用PLINK進行親緣關係的判斷 - 凡走過必留下痕跡
此步驟會產出兩個檔案：indep.prune.in是獨立的SNPs清單；indep.prune.out是具有LD ... plink --bfile raw-GWA-data --extract indep.prune.in --genome --min 0.1875 ... http://rover1023.pixnet.net |