I have a set of many bam files for which I would like to know if an insertion of a few 100bp is present at a certain locus.
The insertion variant is not picked up by small variant callers like freebayes, gatk or structural variant callers like lumpy or manta when doing a full genome variant calling.
It should be possible to use the aligned reads and their unmapped mates to do a full local assembly of the region that includes the insertion.
What tool or pipeline can I best use for this?
I guess I need to use both the bam files and the original fastq files, since I need the unclipped, unsplit reads for the local assembly?