Get sequencing from GTAC. The only file of interest is rawSNP.txt
Use this script to split the initial file into files for each chromosome (and discards most indels) on both your mutant and wt pools.
Use this script to mask these known repeat regions in zv10 (assuming your mapped to zv10) on both your mutant and wt pools.
Use this script to compare the mutant and wt pool.
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