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Andrew Roth edited this page Jan 4, 2017 · 1 revision

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.
  2. 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.
  3. Sorting BAM files. BAM files should be coordinate sorted for use with JointSNVMix. The order of chromosomes in the header should not matter,

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