of reads overlapping the location of
the SNP in question.
Calling structural variations. In addition to small nucleotide changes,
larger structural variations involving
insertion, deletion, and translocation
of large genomic regions are another
important source of genomic variation. Consider the example of deletions in the donor genome (see Figure
2b) in which a large segment of DNA
is deleted, relative to the reference. If
both copies of the donor genome are
deleted, the deletion is homozygous;
otherwise, it is heterozygous deletion.
Deletions are detected through several techniques:
Paired-end mapping. Paired-end
sequencing sequences both ends of
large genomic fragments (sampled
randomly from the donor genome).
These fragments are size-selected
to be tightly distributed around a
specified length L(≈500). If paired
reads end up mapping much further
apart than L (length discordance), a
geneticist can infer a deletion in the
donor relative to the reference (such
figure 3. Layers of genomic processing software.
as read “a” in Figure 2b). If the deletion is heterozygous, the geneticist
would see a mix of concordant and
discordant reads at the breakpoints
of the deletion.
Depth of coverage. “Depth” at a
position refers to the count of reads
mapped to the position. Deleted regions of the donor chromosome will
have reduced coverage—roughly half
for heterozygous deletions and zero
for homozygous ones. Thus, read “b”
in Figure 2b maps within the deleted
region, but reads “a” and “c” do not.
abstract of two
CNVer, SV detection tools
e.g., fast iP
internet Protocol (iP)
Examples: SlimGene, BAM
Examples: MAQ, bwa
Life Tech, Roche, PacBio
C:30M:00Y:100K: C:00M:00Y:00K: 35 C:00M:85Y:90K:00
C:20M:00 Y:100K: C:00M:00 Y:00K: 100 C:00 M: 100 Y: 100