Hello,
I have been reading through everything I can find that relates to this
subject, but I'm still unsure if I understand things correctly.
Picard and samtools now recognize the 0x800 flag and deal with it
accordingly, but what does this mean exactly? Does it mean that those reads
are outputted unchanged or that they undergo the same process of the other
reads?
Also, if downstream tools recognize and deal with the 0x800 flag, we should
no longer use the -M option in bwa mem otherwise we are just setting all
those reads to 0x100, right? Unless, the tools only ignore the 0x800 flag
and then having it set to 0x800 or 0x100 doesn't make any difference,
correct?
Can someone clarify this for me? And is there any command within picard
and/or samtools which is still not updated to deal with supplementary
alignments?
Thank you,
Ines.
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