What is the difference between the title mentaioned alignment reads?
Linear Alignment: An alignment of a read to a single reference sequence that may
deletions, skips and clipping, but may not include direction changes (i.e. one portion of the alignment
on forward strand and another portion of alignment on reverse strand). 1
Chimeric Alignment: An alignment of a read that cannot be represented as a linear alignment. 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. 1
Representative alignment: A chimeric alignment that is represented as a set of linear alignments that do not have large overlaps typically has one linear alignment that is considered the representative alignment. 4
I don’t understand representative alignment with the word “representative” in my mother tongue and could not find more information(figure) about it.
It seems that GATK can realignment those representative reads to the correctly position via
RealignerTargetCreator and IndelRealigner. (WARNING: I am not quite sure if I understand this correctly. If someone could help me, please leave me a message below, thanks, thanks.)
Supplementary Alignment: A chimeric reads but not a representative reads.
Primary Alignment and Secondary Alignment: A read may map ambiguously to multiple locations, e.g. due to repeats. Only one of the multiple read alignments is considered primary, and this decision may be arbitrary. All other alignments have the secondary alignment flag. 5
How to filter those reads?
I usually use samtools to filter those reads. Picard tools website provide a online SAM flags explaination tool.
samtools view -f/-F command can
filter out the reads with specific flags.