Looks for reads with mutation at known positions and calculates frequencies and stats.
va_macros.xml
xlsxwriter
`_.
**Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the
tool `Map with BWA-MEM `_.
**Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool
containing dictonaries of the tags of reads containing mutations
in the DCS.
**Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool
stats of tags that carry a mutation in the SSCS at the same position a mutation
is called in the DCS.
**Output**
The output is an XLSX file containing frequencies stats for DCS mutations based
on information from the raw reads. In addition to that a tier based
classification is provided based on the amout of support for a true variant call.
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