Two follow-up questions for BioStar:
1) I used Picard "MarkDuplicates" to mark duplicates and called bam as "marked.bam". I used snpeff to annotate snps and indels etc. The file written using marked.bam is smaller than un-marked bam (~5000 rows smaller). So I am assuming snpeff is not taking into account PCR duplicates. Is this correct?
2) Now I want to compare snpeff result between two samples. ANy recommendations for softwares for this? I obviously will compare SNP and INDELS etc.
Thanks very much again. *[Edited]