/zebrafish_pipeline

UNDER CONSTRUCTION

Primary LanguageRuby

Zebrafish BWA/PicardTools/GATK pipeline

This pipeline is suppose to automate all the necessary steps between raw sequenced data and called variations.

Note: This gem is under construction!

The steps

Aligning the fastq files containing the raw sequenced data with bwa

This gem is using the Burrows-Wheeler Aligner(BWA) to map the short reads back to the genome. This involves two steps:

  1. bwa align
  2. bwa samse for single- or bwa sampe for paired-end reads

BWA is used with default settings.

Bam-file Conversion/Sort/Index with Picard tools

Using Picard tools to add read groups

Marking duplicates in each of the samples (picard tools)

(Merge all the .bam files)

Realigning with GATK

Recalibration

Unified Genotyper

Evalution of .vcf files