is it mandatory to use fixmate?

Question

[rj.rezwan]

Hi, I mapped the paired-end reads of different accession on the reference genome using BWA. The calculated mapping summary depicted the good proper pairs mapping %. Afterward, I sorted the files as abc_sorted.bam. So is it mandatory to go through the fixmate in Picard prior to using markduplication tool in Picard?

Answer 1

[barslmn]

I don't think Picard requires fixmate before markduplicates but samtools does.