Flávia Eichemberger Rius flaviaerius

## bcftools.md

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                flaviaerius
                / bcftools.md
            
            
              Last active
              November 27, 2023 16:54
                — forked from elowy01/BCFtools cheat sheet
            
              
                BCFtools cheat sheet
              
          
    View

Printing out info for only 2 samples:

bcftools view -s NA20818,NA20819 filename.vcf.gz
Printing stats only for variants passing the filter:

bcftools view -f PASS filename.vcf.gz
Printing variants without header:

bcftools view -H

  
## install-samtools-bcftools-and-htslib.md

      
              1 file
            
          
              1 fork
            
          
              0 comments
            
          
              0 stars
            
          
                flaviaerius
                / install-samtools-bcftools-and-htslib.md
            
            
              Last active
              March 11, 2024 17:40
                — forked from adefelicibus/install-samtools-bcftools-and-htslib.md
            
              
                Install samtools, bcftools and htslib on linux
              
          
    Install samtools, bcftools, htslib, bedtools, and plink2 on linux

Install some build dependencies

sudo apt update

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev wget libncurses5-dev bzip2