I have made a whole assembly of RNA seq data using Trinity. The assembled file generated has been aligned with my choice of dataset to identify SNPs. The first step was alignment which I have manged to do by using BWE. But I am experiencing some problems in this output which is in the form of BAM file. I tried to Add or replace read groups using 'NGS Piccard' . When I try to visualise it in IGV it said
"Cannot add sequence that already exists in SAM Sequence Dictionary"
In order to resolve this I want to clear and edit the headers. I am not able to find which will be a suitable tool to for this.
Any suggestions what can I do?
Can anybody please tell me what this means and why is this error coming from?