I have a Human genome sequenced in a BAM file (along with other files with the indels, snps, cnvs).
I want to find every mutation with regards to the reference Human genome. However the majority of "variants" are noise/read errors. I am therefore required to filter the variants via a minimum threshold based on allele freq (eg. 0,5).
Using a reference (eg Hg19), how can I find the position of every mutation where the allele frequency is greater than the threshold?
PS. I am just starting, so I don't know which are the best (command line?) tools for the job nor how to build a pipeline for this.
Help would be greatly appreciated