I have mapped some reads to a reference and want to change SNPs in the reference to SNPs found in the reads, even at low coverage. For example, here is a screenshot of one reference in IGV that I would like to correct.
When I use pilon to try to correct the reference, however, no bases are ever changed, even if using the option --mindepth 1
.
Here is the call that I am using:
java -Xmx100G -jar {params.pilon}\
--genome {input.ref}\
--frags {input.bam}\
--output {params.outname}\
--changes --fix all,amb,breaks,bases\
--threads {threads}\
--mindepth 1
How can I use even low-coverage information to correct my reference?