perform evolutionary or population-based analyses directly on BAM/SAM files

POPBAM, http://popbam.sourceforge.net/

POPBAM is a tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can computemany widely used evolutionary genetics measures in sliding windows across agenome. The motivation for developing POPBAM is to provide the community with afundamental suite of evolutionary analyses tools that would otherwise be tedious toimplement. Since POPBAM works directly with BAM files, there are no intermediarysteps necessary.

To enable POPBAM to perform population-level analyses, it is first necessary to modify the input BAM file header. Users must add the "PO" tag to the header line for each read group. The "PO" tag can be any string, as long as the string is identical between samples from the same population. One example may be that a BAM file has three read groups (R21, R22, and R25). The R22 and R25 read groups are from two different lines of Drosophila melanogaster called "MEL01" and "MEL02", while the third read group, R21, is from a single line of D. simulans called "SIM01". Below is an example of the BAM header including the "PO" tag:

@RG  ID:R22  SM:MEL01  PO:MEL
@RG  ID:R25  SM:MEL02  PO:MEL
@RG  ID:R21  SM:SIM01  PO:SIM