ReadCounts tabulates the number of reads providing evidence for variant and reference nucleotides at specific genomic loci and applies statistical tests to recognize allelic read-counts consistent with homozygous and heterozygous loci.

ReadCounts is available as a self-contained binary package for 64-bit Linux and MacOS/Darwin systems and as Python source. The pysam package, plus a variety of common third-party python packages including numpy and scipy must be installed to use ReadCounts in Python source form. See the install instructions for more details. The self-contained binary package is appropriate for most Linux and MacOS users.

Setup:

• Download
• Install

Usage:

• ReadCounts

File Formats:

• Input Files
• Output Files