Hi Xinan,
I'd also like to have a clearer definition of at least NH.
In Novoalign we have interpreted NH as the number of alignments to the
query sequence that are equivalent to the best alignment. These may not all
be reported in the SAM file.
So if we find 100 alignments but create SAM records for only 10 then NH is
100 and IH is 10.
I've never checked what other aligners do with NH.
Kind Regards, Colin
On 21 May 2014 21:47, Xinan Liu <hitcs...@gmail.com> wrote:
> Hello,
>
> I am a little confused about the difference between NH and IH tags in
> SAM format.
>
> NH: Number of reported alignments that contains the query in the current
> record
> IH: Number of stored alignments in SAM that contains the query in the
> current record
>
> Some aligners are using NH, and some other aligners are using IH. So
> what's the difference between them? Thanks.
>
> --
> Xinan Liu
>
>
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