Table 1

Decision table for merging of read alignments

Genome mapping

CCDS mapping

Agree?

Hard merge

Soft merge

Unique

Unique

Yes

Keep

Keep

Unique

Unique

No

Throw

Throw

Unique

Multiple

No

Throw

Keep

Unique

Not mapped

No

Keep

Keep

Multiple

Unique

No

Throw

Keep

Multiple

Multiple

No

Throw

Throw

Multiple

Not mapped

No

Throw

Throw

Not mapped

Unique

No

Keep

Keep

Not mapped

Multiple

No

Throw

Throw

Not mapped

Not mapped

No

Throw

Throw

Duitama et al. BMC Genomics 2012 13(Suppl 2):S6   doi:10.1186/1471-2164-13-S2-S6