Hi pals,
I have already preprocessed bam file that has duplicates marked, realigned and BQSR performed by GATK.
Because of some reasons, I need to remove the duplicates.
Is it a good idea to remove duplicates on the analysis ready bam file, rather than repeating entire preprocessing with duplicates removal ?
If I remove the duplicates from analysis-ready bam, will it be necessary to perform realignment and BQSR again ?
Thanks
I have already preprocessed bam file that has duplicates marked, realigned and BQSR performed by GATK.
Because of some reasons, I need to remove the duplicates.
Is it a good idea to remove duplicates on the analysis ready bam file, rather than repeating entire preprocessing with duplicates removal ?
If I remove the duplicates from analysis-ready bam, will it be necessary to perform realignment and BQSR again ?
Thanks