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Old 10-17-2011, 10:02 AM   #9
skruglyak
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Location: San Diego

Join Date: Sep 2010
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Quote:
Originally Posted by maubp View Post
Hi Semyon

Could you clarify if the unaligned reads in SAM/BAM format from Illumina CASAVA 1.8.x have FLAG bit 0x200 (not passing quality controls) set according to your non-PF QC?

Thanks,

Peter
Hi Peter,

There is a distinction between unaligned reads and non-PF reads.
In CASAVA 1.8 all non-PF reads in the BAM output have the "not passing quality controls" flag bit set (0x200). Note that this setting is independent of alignment -- unaligned reads are indicated with the conventional "segment unmapped" flag bit (0x004). Starting in 1.8.2,the default behavior will be to exclude non-PF reads entirely as explained earlier in the post.

Thanks,
Semyon
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