I am working on variant calling on fungal genomes. I have Illumina HiSeq reads. I am new to this and am following this workflow
Step 1: QC of raw reads performed using FastQC tool
Step 2: Preprocessing of raw reads performed using Trimmomatic-v0.36 tool
Step 3: QC of clean reads performed using FastQC tool
Step 4: Alignment to reference genome using bowtie2-v2.2.6 tool
Step 5: SAM to BAM (alignment files) conversion using samtools-v1.3.1
Step 6: Remove duplicates using sambamba-0.6.6 tool
Step 7: coordinate sorting of bam files with samtools
Step 8: Variant calling performed using samtools/bcftools
Step 9: variant filtering with bcftools
In this post Workflow Or Tutorial For Snp Calling? and other variant calling related resources I found 2 additional steps before variant calling i.e. local realignment and base quality recalibration.
- Are these steps essential?
- I found that these option are not available in samtools but in GATK. How can I perform these steps for my data?