See the Order of operations page for more details.
The first four columns are from the MAP file (chromosome, SNP ID,
I thought about using the bim file as a reference for the order that PLINK will use, but I am
This function call will write output files in PLINK.
How to convert data into the PLINK 1 binary format.
By default, bedtools sort sorts a BED file by chromosome and then by start position in ascending order. For example: cat A.bed chr1 800 1000 ...
The mask file contains a sequence of integer digits (between 0 and 9) for each position on a chromosome
Also note that chromosome ordering in FILE will be respected, the VCF
Suppose we had some PLINK format data called data.bed, data.bim, and data. fam.
plan to retain VCF format for the output, I recommend against using PLINK.