I am looking at the
bwamem.h code in http://github.com/lh3/bwa and found that BWA-MEM will give flag 0x200 to what it calls
#define MEM_F_PE 0x2 #define MEM_F_NOPAIRING 0x4 #define MEM_F_ALL 0x8 #define MEM_F_NO_MULTI 0x10 #define MEM_F_NO_RESCUE 0x20 #define MEM_F_REF_HDR 0x100 #define MEM_F_SOFTCLIP 0x200 #define MEM_F_SMARTPE 0x400 #define MEM_F_PRIMARY5 0x800 #define MEM_F_KEEP_SUPP_MAPQ 0x1000
But looking at the explanation in this website: https://broadinstitute.github.io/picard/explain-flags.html
0x200 as read fails platform/vendor quality checks.
If we have reason to believe that soft clipping can happen for some of the alignments, should we just ignore the fact that IGV calls this fail QC? Does the failQC tag come from the SAM/BAM specification or is this something IGV came up with?
The SAM/BAM specification labels
0x200 the same way as the Picard flag explaining website:
The question remains as to why BWA-MEM uses the
0x200 flag for softclipping notation rather than Fail QC.