Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs...
...racting with high-throughput sequencing data. It consists of three separate repositories:
SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReading/writing...
...Count bases in a SAM/BAM/CRAM file
CountBasesSpark...Count reads in a SAM/BAM/CRAM file
CountReadsSpark...Tools that manipulate read data in SAM, BAM or CRAM format
AddCommentsToBam...