mcanouil

# # MIT License
#
# Copyright (c) Mickaël Canouil
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:

variani

# ------------------
# from bgen to bed
# ------------------
plink2 --bgen myfile.bgen \
  # filter by chr or by snps names
  --chr 1 --extract {params.snps} \ 
  --make-bed --out myoutput
# 1. plink will create temporary/intermediate files such as *-temporary.{pgen,psam,pvar}
# 2. sample ids in .fam will be `ID1_ID1`

sinarueeger

Extract genetic data for a subset of SNPs

Below are instructions on how to extract single SNP data from large genetic datasets.

• Genotype data (*.map, *.ped or *.bed, *.bim,*.fam)
• Gentoype imputed data (*.gen or its binary version: *.bgen)
• Sequencing data (*.vcf.gz)

More on genetic data file formats here.

dlfinis

The syntax of sed command replacement is:

$ sed 's/find/replace/' file

 This sed command finds the pattern and replaces with another pattern. When the replace is left empty, the pattern/element found gets deleted.

Let us consider a sample file as below:

$ cat file
    Linux