I am newbie to NGS data analysis.
I used BWA for aligning to reference genome and then samtool. Now am having bam file, sam file and VCF file. i used IGV browser to view the bam file in than i seen IGV uses color coding to flag anomalous insert sizes.
Red for an inferred insert size that is larger than expected (deletion) Blue for an inferred insert size that is smaller than expected (insertion)
i need to extract the deletion part from the bam file or samfile. can anybody give a suggestion of tools on how to extract this particular region ?