SUFAM v0.4.2

<p><strong>S</strong>o yo<strong>U</strong> think you <strong>F</strong>ound <strong>A</strong> <strong>M</strong>utation (<strong>SUFAM)</strong>? SUFAM reports the mutant allele fraction (MAF), read counts and coverage of a given variant or mutation in a SAM/BAM/CRAM file. It is a Python wrapper around <em>samtools mpileup</em> that makes it straightforward to determine the MAF of a given mutation. Parsing the output of <em>samtools mpileup </em>is error prone, while SUFAM has been rigorously tested to confirm it's correctness in a wide range of cases. A command line interface as well as a Python API are provided. The tool has proven to be immensely useful in a variety of cases e.g. validating called mutations from exome sequencing data in RNASeq data, confirming mutations in BAMs from The Cancer Genome Atlas (TCGA) and finding mutations in extremely low abundance in DNA sequencing data from blood plasma.</p