Question: What does secondary (and some other fields) mean in flagstat output?
gravatar for Niek De Klein
5.1 years ago by
Niek De Klein2.5k
Niek De Klein2.5k wrote:

This is my samtools flagstat output for the alignment of a paired-end sample using HISAT (filtered with MQ<1):


45084184 + 0 in total (QC-passed reads + QC-failed reads)
4717987 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
45084184 + 0 mapped (100.00%:-nan%)
40366197 + 0 paired in sequencing
20273012 + 0 read1
20093185 + 0 read2
39146254 + 0 properly paired (96.98%:-nan%)
39644363 + 0 with itself and mate mapped
721834 + 0 singletons (1.79%:-nan%)
260722 + 0 with mate mapped to a different chr
235361 + 0 with mate mapped to a different chr (mapQ>=5)


There's quite a few questions about flagstat on Biostars, but I haven't seen the secondary, supplementary or duplicates flag before. Assuming that this is HISAT specific, are is secondary the number of mapped reads that get mapped using the second (non-global) HISAT index? What would supplementary mean? And are duplicates the amount of reads that map non-uniquely?

samtools flagstat • 7.8k views
ADD COMMENTlink modified 5.1 years ago by Devon Ryan96k • written 5.1 years ago by Niek De Klein2.5k
gravatar for Devon Ryan
5.1 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

These are defined more formally in the SAM specification, though perhaps the wording there isn't great.

Secondary: One of the many places a multimapper can align. Note that multimappers will have one primary and 0 or more such secondary alignments.

Supplementary: For chimeric/fusion/non-linear alignments, this is the location of one part of the alignment. For reads that align in a chimeric fashion, one segment will be designated as primary and the remainder supplementary.

Duplicate: If you've marked possible PCR duplicates, then this will be set. The definition of a duplicate is somewhat dependent on the tool used (N.B., aligners don't typically set this flag, it's down by picard's markDuplicates command or similar).

ADD COMMENTlink written 5.1 years ago by Devon Ryan96k
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