In the variant calling pipeline(i.e. GATK), after reads mapping, there are, in general, several steps before variant calling. 1) mark duplicates, 2) realignment (as far as I know it is important for small INDEL variants), 3) base recalibration
1) There is a parameter in pilon --duplicates. Should I run i.e. Picard to mark duplication reads before running pilon?
2) Pilon document mentioned, there is a left alignment method implemented, so I do not need to run realignment software anymore, am I right?
mjmillerlab
commented
4 years ago
In the variant calling pipeline(i.e. GATK), after reads mapping, there are, in general, several steps before variant calling. 1) mark duplicates, 2) realignment (as far as I know it is important for small INDEL variants), 3) base recalibration
1) There is a parameter in pilon --duplicates. Should I run i.e. Picard to mark duplication reads before running pilon? 2) Pilon document mentioned, there is a left alignment method implemented, so I do not need to run realignment software anymore, am I right?