The difference between scanBam and readBamGappedAlignments

[linahao]

Hello there,

I am extracting short reads from a .bam file in one specific region using Bioconductor Rsamtools package, the sequence information from scanBam and readBamGappedAlignments are different. Could somebody please tell me what is the difference of scanBam and readBamGappedAlignments? Many thanks!!

[Dario1984]

Use readBamGappedAlignments if some of your mapped reads are spliced.