bash-scripts

Bash scripts used in the analysis of Illumina sequence data:

1) trimmomatic.sh

• Removes Illumina sequencing, and other, adapters and trims poor quality reads

2) bwa.sh

• Aligns reads to the reference genome and generates the .sam file required for variant calling

Understanding variant information in a .vcf file

• col9 FORMAT > GT:AD:GQ:PL

  GT: genotype [0 (REF), 1 (ALT), 2 (2nd ALT etc.), | (phased), / (unphased)]

  AD: allelic depth [# reads w/REF vs. ALT base]

  GQ: genotype quality [phred score]

  PL: phred-scaled genotype likelihood [1st = p(site is homozygous-REF), 2nd = p(site is heterozygous), 3rd = p(site is homozygous-ALT)]