LinuxCommands.md

Basic Linux commands

Count files in folder using list (ls) and word count (wc)

ls /path | wc -l

Check folder size (du)

du -sh /path

Copy files or folder from server using scp (-r copy folder)

# scp -r [FROM:PATH] [TO:PATH]

scp -r username@192.168.0.1:/path/ /path

scp username@192.168.0.1:/path/file /path

Read length of fastq file

echo $(zcat *.fastq.gz|wc -l)/4|bc

BASH

Nested loop

Set location and run nested loop example

#!/bin/bash

inp_loc="/Users/path"
cd $inp_loc

#trim adaptor for all fastq files
for i in $(eval echo {A..D}); do
  for x in {1..5}; do
      print${i}${x}
    done
done

BCFTools

Manual:

https://samtools.github.io/bcftools/bcftools.html#view

View

View VCF file

bcftools view file.vcf.gz

Extract specific chromosome data

bcftools view file.vcf.gz --regions [CHROM NAME] > output.vcf

bgzip output.vcf

Filter on minor allele frequency MAF

bcftools view -q 0.05:minor pop.vcf.gz > popMAF.vcf

Merge:

Merge VCF files

ls *.vcf.gz > merge.txt

bcftools merge -l merge.txt -0 -Oz -o pop.vcf.gz

Index:

View per contig stats (SNPs)

#multi loci file
bcftools index -s input.vcf.gz

#single loci file
bcftools index -n input.vcf.gz

Create VCF index files

bcftools index file.vcf.gz

Fasta Alternate Reference Maker

Create reference sequence dictionary

java -jar /home/jhetzler/tools/picard/picard.jar CreateSequenceDictionary R=../ref/reference.fasta O=../ref/reference.dict

Create index files for vcf

gatk IndexFeatureFile -I A1.vcf.gz

Create an alternative reference by combining a fasta with a vcf.

https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker

gatk FastaAlternateReferenceMaker -R /home/jhetzler/MiSeqOSL/ref/reference.fasta -O A1_FARM.fasta -V A1.vcf.gz