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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Pilon on haplotype polish: how did pilon deal with haplotype genome assembly? #143

Open cjchen5 opened 2 years ago

cjchen5 commented 2 years ago

Hi, I'm working on applying pilon to polish haplotype genome assembly, but I only have diploid Illumina data. I'm wondering how pilon deal with the diploid genome when it only polish one haplotype genome while using diploid short reads. I found this description but I'm wondering how to define the vast majority? Is there any way to let me set the parameter for the vast majority of evidence?

From the pileup evidence, Pilon classifies each base in the input genome into one of four categories:
Confirmed: the vast majority of evidence supports the base in the input genome;
Changed: the vast majority of evidence supports a change of the base in the input genome to another allele;

Thanks!