Plantenthusiast

As I have discussed in the previous blog, we already have aligned SAM (.sam) file to be further utilized for analyzing genomic variations. In this post, I am going to instruct the steps involved in the analysis of genomic variations among the closely related organisms. In particular, I am presenting the workflow pipeline for the GATK (Genome Analysis Tool Kit) HaplotypeCaller for detecting SNP (Single Nucleotide Polymorphism) sites and their annotation by snpEff .  Note: In order to carry out SNP sites detection by GATK, there should be SAM file of the whole genome sequence of an organism, preinstalled GATK software version  4.1.0.1  and above  (McKenna et al., 2010)  with its accessory packages, Samtools, and snpEff   4.3t   (Cingolani et al., 2012)  in Linux server. Image 1. a screenshot of a home page of gatk website (source: https://software.broadinstitute.org/gatk/) In brief 1. get the SAM file of the whole genome sequence of the sample organism; 2. do SNP

Since the aim of this blog is to share the information on various aspects of plants and plant sciences, this time, I am blogging about the bioinformatics tools that help study about the genome of organisms including plants.    The application of  BWA  software or any other software that allows alignment of fastq (.fq) files of the sample genomic DNA sequence to  reference genome  is an essential step before carrying out further investigations such as the genome analysis. In this post, I am going to present the instruction for the alignment of quality trimmed fastq (.fq) files of a sample genome to the reference genome using BWA (Burrows-Wheeler Aligner) software. This instruction covers installing of BWA software, indexing the reference genome, quality trimming the raw fastq files, and aligning the quality trimmed  fastq  files to reference genome to get  SAM  (Sequence Alignment Map) file of a sample genome.  Image 1. The vines of Vitis vinifera cv. 'Pinot Noir' with be