Quick question: samtool idxstats and multiple mapping

Question

[Aurelie MLB]

Hello,

A quick naive question please: Samtools idxstats outputs the number of reads mapped to a given reference sequence. Right? What does it do in case of multiple mapping please? Does it count the best alignment for a read or does it adds 1 to all reference sequences where it mapped? I could not find any detail in the documentation.

Many thanks

[cpad0112]

samtools idxstats outputs total mapped. If you would like to see secondary alignments, try flagstat from samtools. It would print secondary alignment.

Answer 1

[Devon Ryan]

As cpad0112 mentioned, every alignment is counted, whether secondary or supplementary. So if a read has multiple recorded alignments then each is counted.

BTW, this is only true of BAM files. For CRAM files on 0 will be returned.

[Aurelie MLB]

Thank you so much to both!! Really helpful!!

[cc3423]

Hi Devon, Thanks for the reply. Is there any documentation about the multi-mapped you could share? I am wondering whether every method in samtools/sambamba take the XA flag into account; or it is specific for idxstats in samtools.

[Devon Ryan]

Whether a read is multimapping or not is determined by the aligner (it sets a bit in the FLAG field in the SAM/BAM/CRAM output). Samtools is just reporting whatever the aligner wrote. The XA tag is a custom tag produced by a couple aligners, almost all tools (including samtools) will ignore it completely.