WebbI've tried to merge two data files (binary) with genome wide SNP data but I've got a few hundred warnings: plink --bfile file1 --bmerge file2.bed file2.bim file2.fam --make-bed --out join2 ... Webb14 apr. 2024 · I have a SNP multi-sample vcf file (n=259 people) from target exome sequencing with ~20x coverage; this file has been processed with GATK by a big Center so I fairly trusted their work. This multi-sample vcf file contains ~70 close relatives (mostly siblings,1st cousins, parents), so I expect king to estimate the relatedness accurately.
PLINK 2.0 - cog-genomics.org
Webb1 dec. 2024 · plink2.0主要是从以下几个方面,相对于plink1.9有较大的提升: 1,保留参考等位基因的信息,比如vcf格式的数据,不要添加参数 --keep-allele-order。 这样vcf变为plink,plink变为vcf就可以不用指定ref和alt了,切换无障碍! 2,新的.pgen文件,结合SNPack-style的压缩,可以节约80%的文件大小。 比如1000个Genomes,比压缩的gzip … Webb24 aug. 2024 · I would reccomend using bcftools on the original vcf files before you convert them to plink, to fill in missing IDs using the command: bcftools annotate --set-id … aggiustalo
How can I create a UCSC BED file from plink data?
Webbwith answers that suggest "plink --vcf" with VCF as input. (Internet search for "convert vcf to plink" might also be informative.) Unfortunately, my suggested command for translating VCF... Webb11 apr. 2024 · plink2 --pfile binary_fileset--export bgen-1.1 --out new_text_fileset. generates new_text_fileset.bgen and new_text_fileset.sample from the data in binary_fileset.pgen + … Webb16 nov. 2024 · to plink2-users Three options: 1. Use --make-pgen/--pfile instead of --make-bed/--bfile. This is the preferred solution if it's compatible with your workflow. 2. Filter multiallelic variants... aggiusta frasi