bwa mem without -M option how to continue using picard

Question

[Peter Chung]

I do the alignment without -M option and now I have all the bam file and would like to do the downstream steps using picard and GATK, what can I do to restore the -M option except realign all the fastq because I have more than hundreds fastq files. Thank you

Answer 1

[d-cameron]

This can be achieved with software that can edit SAM files (such as samtools and sambamba)

You want to set the secondary alignment flag (0x100) for all reads that have the supplementary alignment flag set. (0x800).

Answer 2

[dariober]

Is it still the case that picard (MarkDuplicates?) chokes on split reads? I would check that first. Using -M option is a hack to make picard work but it would be better avoiding it since the shorter split of a read is not a "secondary alignment" and there is nothing necessarily wrong with split reads. They may be the result of structural variants.