BAM Manipulation

Perform various utility functions on BAM files (e.g. index, sort, remove duplicates, merge, filter).

Tool Name	Input	Output	Description
bam-indexer	BAM	BAI	Generates BAI Index for input BAM files. Output BAI is in the same directory as input BAM file.
sort-bam	BAM	BAM	Sort BAM files in order to efficiently extract and manipulate.\nRAM intensive process. If program freezes, increase JAVA heap size.
mark-duplicates	BAM	BAM	Removes duplicate reads in Paired-End sequencing given identical 5' read locations. RAM intensive process. If program freezes, increase JAVA heap size.
merge-bam	BAM[..]	BAM	Merges Multiple BAM files into single BAM file. Sorting is performed automatically. RAM intensive process. If program freezes, increase JAVA heap size.
filter-pip-seq	BAM	BAM	Filter BAM file by -1 nucleotide. Requires genome FASTA file. Note this program does not index the resulting BAM file and user must use appropriate samtools command to generate BAI.