I am looking at the error rates of a particular Illumina sequencing project. I have the bam files from the project and want to see the mismatches and indels in the reads compared to the reference genome. The data is pair-ended and PCR-free. I thought I needed to call all the variants in the alignment by
(1) filtering out poor quality alignment
(2) not filtering out poor quality variant calls
with a regular variant caller. I like freebayes but I guess any caller would do. I considered using the following options:
freebayes -f reference.fasta -F 0.01 --min-alternate-count 1 --min-alternate-fraction 0.01 alignment.bam
Are my parameters correct? Does my idea even make sense?