I am trying to work out what tools use the secondary alignment feature of the sam format. My understanding is that there will always be exactly 1 primary alignment for each read, and secondary alignments could arise because the aligner cannot decide the exact best alignment.
Does BWA / other aligners emit secondary alignments?
Which downstream tools use secondary alignments? Haplotypecaller?
1 answer
For RNAseq quantification, RSEM, eXpress and Salmon (when quantifying reads from BAMs) include secondary alignments in their quantification. Probably all mappers output secondary alignments, but implementation details may vary, and often there are flags to alter this behaviour. For example, bwa mem -M will mark shorter split hits as secondary instead of suplementary, or STAR --outSAMprimaryFlag AllBestScore will mark all multiple alignments with the same best score as primary.
I am not aware of other tools that use secondary alignments, but this doesn't mean they don't exist.
Log in to answer this question.
-
Is comparing seeds sufficient, or should alignments be compared instead?
written by curiousfellow@123 •
-
vg giraffe handling of second vs. supplemental/split alignments, novel SVs, and associated MAPQ
written by Thomas •
-
What aligners to choose between Hisat2 and BWA for chip-SEQ analysis
written by Molinia •
-
One read and One alignment
written by cxr5298 •
-
filtering reads that are uniquely mapped
written by Florian Bernard
-
SAM / BAM alignments
written by John
-
report all possible alignments
written by cmo
-
Split Contig Structural Variant Calling On Bac Contigs Aligned With Bwa-Mem.
written by William
-
Why Is Tophat Reporting Secondary Alignments Even When The Option To Do So Is Turned Off
written by Varun Gupta
-
The Role Of Alignment In Processing Sequencing Data
written by KCC
