MarkDuplicates output file in GATK pipeline

Question

[gprashant17]

I have used GATK's MarkDuplicates on a BAM file I obtained after alignment, which resulted in another file marked_duplicates.bam. So should I proceed with this marked_duplicates.bam file for analysis (converting to VCF), or this is just a file containing duplicates? In the latter case, is it possible to obtain a BAM file, with all the duplicates removed?

Answer 1

[Pierre Lindenbaum]

So should I proceed with this marked_duplicates.bam file for analysis (converting to VCF),

yes. As a proof, test both files wth samtools flagstats

is it possible to obtain a BAM file, with all the duplicates removed?

in the manual : https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.4.0/picard_sam_markduplicates_MarkDuplicates.php#--REMOVE_DUPLICATES

--REMOVE_DUPLICATES / NA

If true do not write duplicates to the output file instead of writing them with appropriate flags set.

[gprashant17]

So if I did not use --REMOVE_DUPLICATES, the duplicate reads will still be present in the marked_duplicates.bam but they would have been flagged as duplicates right?

[Pierre Lindenbaum]

So if I did not use --REMOVE_DUPLICATES, the duplicate reads will still be present in the marked_duplicates.bam but they would have been flagged as duplicates right?

yes