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Thunder

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minDepth and maxDepth are the cutoffs on total depth (across all individuals). We have found it useful to exclude sites with extremely low and high total depth. Please see Important Filters below.
=== (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V009V010.source.tgz thunder_glf_freq] ===
thunder_glf_freq --shotgun my.out.$chr -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out
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