Q:

I would like to ask about what kind of indels are incorporated into the
diploid genome assembly of the NA12878 individual, available from your lab:

http://sv.gersteinlab.org/NA12878_diploid/NA12878_diploid_dec16.2012.zip

In the readme it says that 829,454 indels were used to construct this
genome. What makes me confused is that when I perform a BLAST search with
one 1.7 kb deletion from NA12878.2010_06.and.fosmid.deletions.phased.vcf
(P2_M_061510_21_73), it shows up in both the maternal and paternal
haplotypes. Is there any size cutoff used for the indels that have been
selected for this assembly?

A:
in the latest version no fosmid indesl/SVs were used. Only output of GATK.