hello everyone, I'm new to bioinformatics and I'm developing a pipeline to identify variants in target re-sequencing. I thought about doing the analysis like this: fastq --> quality analysis with fastqc--> hg19 alignment with BWA MEM --> sam to bam with samtools-> sorted and indexing bam with samtools--> variant calling with vardict or mutect2. I decided not to perform the trimming because they are Ion Torrent data and I read the manual that ubam-ion torrent-files have already had trimmed. furthermore I have not even performed the deletion of duplicates because the sequencing library is based on amplicons and therefore I believe that deleting duplicates is harmful. unfortunately in the call of the variants I have too many variants even limiting the search areas using a bed file and filters, I believe this is due to the presence of false positives which I do not know how to eliminate except by eliminating the duplicates.
could someone suggest me the right way to proceed? thanks a lot! Sara