# FAQ #
  1. **Indexing BAM files**. BAM files must have an index file in the directory alongside them. This can be done using `samtools index`. If there is no index you will receive an error such as `ValueError: no index available for pileup`.
  1. **Pysam compatibility**. The JointSNVMix 0.7.x series is only compatible with pysam version 0.5.0. Using other versions of Pysam will cause errors such as `ValueError: csamtools.Samfile`.
  1. **Sorting BAM files**. BAM files should be coordinate sorted for use with JointSNVMix. The order of chromosomes in the header should not matter,