Due to the PCR based amplification, we need to trim to primers off the PE reads.
However, it seems that the trimming process might bring in low quality in tails, especially that some reads might even fall into Q15-Q20, which might lead to low Quality using GATK variant calling.
`$cutadapt -q 10 -g file:$fprimer -G file:$rprimer --minimum-length 20 $read1 $read2 -o $read1_trim -p $read2_trim`;
The command listed above is the one I used in my calling pipeline, although I can adjust the q to 30, there would be quite a lot reads to be removed.
Is there any smarter method to trim the primers?