Open rorycraig337 opened 6 years ago
I'm finally catching up on long overdue Pilon support. Thanks for writing. I do not have an optional argument to control the size range of indel corrections with "--fix bases". However, those are called based on alignment pileups, so if you could set up the parameters of your aligner to penalize large indel calls within a read, that would prevent Pilon from seeing those. I'll keep this in mind as a future option!
Hi,
I am interested in using RNA-seq data along with standard short reads to polish, and I saw a previous issue that suggested this may be possible with the option "--fix bases", so that only SNPs and short indels are changed and introns do not get deleted.
I notice in the *changes file that Pilon has deleted some sequences >40 bp, which could conceivably be introns. Is there a way of changing the minimum length of a short indel (say to 10 bp)? And could you say what the default maximum length of indel Pilon will look to change with the "bases" flag is?
Cheers