BAM Statistics

Perform various statistical checks on BAM files (e.g. insert size distributions and coverage correlations).

Tool Name	Input	Output	Description
se-stat	BAM	TXT	Genome-Genome correlations for replicate comparisons given multiple sorted and indexed (BAI) BAM files.
pe-stat	BAM	TXT	Generates Insert-size Histogram statistic (GEO requirement) and outputs BAM Header including alignment statistics and parameters given a sorted and indexed (BAI) paired-end BAM File.
bam-correlation	BAM	TXT	Output BAM Header including alignment statistics and parameters given any indexed (BAI) BAM File.