This is an indirect answer, but when mapping the reads, if you want to capture long deletion events within reads so that they can be called by standard variant callers (rather than CNV/SV programs), I suggest you map with BBMap, like this:

(once, for indexing)

bbmap.sh ref=ref.fa k=14

(for each sample)

bbmap.sh in1=read1.fq in2=read2.fq out=mapped.sam k=14 maxindel=770000 minratio=0.4 bs=bs.sh; sh bs.sh

The actual maximum length of indels that can be detected this way is related to the read length. For insertions, the maximum length is around 50% of the read length. 150 bp reads should be sufficient for a 770kbp deletion. once you map the reads like this, you can visualize the long indels in IGV from the sorted indexed bam file (created by the "bs.sh" shell script, if samtools is installed). You can subsequently call the events like this:

callvariants.sh in=mapped.sam ref=ref.fa vcf=vars.vcf ploidy=1

You can increase read length, if needed, with BBMap's Tadpole or BBMerge, like this:

tadpole.sh in1=r1.fq in2=r2.fq out1=e1.fq out2=e2.fq mode=extend extendleft=50 extendright=50

or, for paired reads with a long insert size:

bbmerge.sh in1=r1.fq in2=r2.fq out=merged.fq outu=unmerged.fq rem extend2=50

These require sufficient coverage, though, because kmers from other reads are used for extension. 13x is barely sufficient, but should work.