search

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
338 stars 60 forks source link

Possible to set minimum indel length for correction? #78

Open rorycraig337 opened 6 years ago

rorycraig337 commented 6 years ago

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

w1bw commented 5 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!