I am dealing with amplicon data, which was obtained from multiplex PCR.
Original primers can largely increase the mapping accuracy, since some amplicons are highly homologous with little difference within primer region.
And since these primers may introduce FAKE SNPs when they are within inserted regions from other amplicons, we want to remove the primers from BAM file.
https://github.com/tommyau/bamclipper can clip the primer sequence, however, it is time-consuming when amplicon is sequenced more than 1000X.
GATK can softly clip the sequence. However, it can also clip the sequence that is similar with the primers, especially those are not the real primers, but the insert sequence.
I am wondering if there is any tool that can quickly clip the real primers.