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is it mandatory to use fixmate?

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?

mapping_summary

picard genome mapping fixmate
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updated by barslmn • barslmn • written by rj.rezwan • rj.rezwan

1 answer

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

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written by barslmn • barslmn

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