Hi all:

I recently got quite confused with two SAM flags got from BWA alignment, which is "**supplementary alignment**" from chimeric alignments and "**not primary alignment**" (or "secondary alignment") from multiple mapping.

**What samtools explain about these two flags is:**
(Refer to https://samtools.github.io/hts-specs/SAMv1.pdf)

A chimeric alignment is primarily caused by structural variations, gene fusions, misassemblies, RNA-seq or experimental protocols. It is more frequent given longer reads. For a chimeric alignment, the linear alignments consisting of the alignment are largely non-overlapping. Typically, one of the linear alignments in a chimeric alignment is considered the "representative" alignment, and the others are called "supplementary" and are distinguished by the supplementary alignment flag.  

In contrast, multiple mappings are caused primarily by repeats. They are less frequent given longer reads. If a read has multiple mappings, all these mappings are almost entirely overlapping with each other. In multiple mapping, One of these alignments is considered "primary". All the other alignments have the "secondary" alignment flag set in the SAM records that represent them.

**However**, I found in my ChIP-seq alignment results got from BWA(without -M option), alignments with "supplementary" flags are with overlaps with "representative" alignments,which I think should be "secondary" alignments as described. For example, I got four alignments for one pair of reads:

HWI-C00135:237:CAR2BANXX:1:1101:6737:91207	163	chr6	144444720	60	61M40S	=	144444728	61	GTACACACATATACACAGTGCTAAGTTCATTGTACACACATATACACAGTGCTAACTTCATTGTACACACATATACACAGTGCTAAGTTCATTGTACACAC	BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	NM:i:1	MD:Z:1C59	AS:i:59	XS:i:0	SA:Z:chr6,144444722,+,33S59M9S,60,2;

HWI-C00135:237:CAR2BANXX:1:1101:6737:91207	2131	chr6	144444722	11	56H45M	=	144444720	-47	ACACACATATACACAGTGCTAAGTTCATTGTACACACATATACAC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB	NM:i:0	MD:Z:45	AS:i:45	XS:i:20	SA:Z:chr6,144444728,-,53M48S,11,0;

HWI-C00135:237:CAR2BANXX:1:1101:6737:91207	2211	chr6	144444722	60	33H59M9H	=	144444728	59	ACACACATATACACAGTGCTAACTTCATTGTACACACATATACACAGTGCTAAGTTCAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	NM:i:2	MD:Z:22G30C5	AS:i:49	XS:i:0	SA:Z:chr6,144444720,+,61M40S,60,1;

HWI-C00135:237:CAR2BANXX:1:1101:6737:91207	83	chr6	144444728	11	53M48S	=	144444720	-61	ATATACACAGTGCTAAGTTCATTGTACACACATATACACAGTGCTAACTTCATTGTACACACATATACACAGTGCTAAGTTCATTGTACACACATATACAC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB	NM:i:0	MD:Z:53	AS:i:53	XS:i:49	SA:Z:chr6,144444722,-,56S45M,11,0;

The 2nd and 3rd alignment with "2131" and "2211" flags are as "supplementary" alignments, however, they are fragments of the other two full-length alignments. I didn't find any reads with "secondary" flags in my results, but all alignments with "supplementary" flags I checked are cases like what I show above.

Can anyone help explain this? Should I remove these "supplementary" alignments to keep uniquely mapped reads? Thanks very much.

Best,
Vanilla

Those are proper supplemental alignments, since there's no way to map the entire reads in a biologically coherent manner. A secondary alignment would occur if those reads mapped elsewhere in the genome (i.e., not overlapping like this).

Anyway, yes, you can go ahead and remove those for most downstream applications. One caveat to this is that you might have a structural variation there (tandem repeat).