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cbg-ethz / shorah

Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)
GNU General Public License v3.0
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how to run local mode #18

Closed homopolymer closed 8 years ago

homopolymer commented 8 years ago

Hi, I am going to perform local analysis. Is it correct that running shorah.py -r 'chr:100-400' to call local mode?

ozagordi commented 8 years ago

shorah.py will start a global run, i.e. local haplotypes plus haplotype phasing. If you want to skip haplotype phasing run dec.py. If read length is ~300, then you might want to run in amplicon mode with amplian.py -r chr:100-400.