As VarScan2 depends on samtools mpileup which allows specifying minimum requirements on base- and mapping quality, no strict filtering is IMHO required. Marking duplicates is a good and accepted option, removing them is unneccessary as mpileup ignores them if flagged appropriately. I prefer samblaster for on-the-fly marking of duplicates. It may or may not save you from some false-positives where PCR has over-amplified certain fragments. There is literature out there that shows that the overall effect is minimal. My preferred pipeline is basically:

bwa mem ${BWA_IDX} in_1.fastq.gz in_2.fastq.gz | \
  samtools fixmate -m -O SAM - - | \
  samblaster --ignoreUnmated | \
  sambamba view -f bam -S -l 0 -o /dev/stdout /dev/stdin | \
  sambamba sort --tmpdir=./ -l 5 -o out_sorted /dev/stdin

This gives you a sorted and duplicate-marked BAM file without any intermediate files.

As for VarScan2, also see this VarScan2 publication (but mind that is is quiet old and some options might be deprecated). Base recalibration and realignment is not explicitly recommended for VarScan and has not (to my knowledge) been shown to be truely beneficial, especially considering the computational expenses. There is quiet some literature on this available. I do not personally use it.

Hello R.A. ,

you will find all type of opinions about these steps. Here are mine ;):

• trimming your data isn't neccessary as long as you overall basequalitys are fine. You will throw away to much data that is usable, especially if the paired reads overlap
• mark duplicates is fine, even if the impact to the whole dataset might be small. There are always region that are prefered amplified.
• realign data and recalibrate base quality are method recommended in the best practice guidelines by GATK. The programs use for that are optimized to work together with the other programs provided by GATK. It isn't said, that it is useful when using other variant caller. Especially the impact of recalibrate the base quality is very low if you haven't low complexity data.

fin swimmer