hi~
I use a 300kb virus genome as ref（the genome has two 30kb repeat gegion），and simulate short reads for ref with 0.05 mutation ratio。I run bwa mem and sort and markduplication with picard，and run pilon , find the two repeat region of output of pilon has changed!! That mean pilon call snpindel in repeat region of ref ?
hi~ I use a 300kb virus genome as ref（the genome has two 30kb repeat gegion），and simulate short reads for ref with 0.05 mutation ratio。I run bwa mem and sort and markduplication with picard，and run pilon , find the two repeat region of output of pilon has changed!! That mean pilon call snpindel in repeat region of ref ?