Re: [MUMmer-help] deltafilter -q (was: overlapping matches when calling mummer -mum)

[Adam P. <aph...@gm...>]

delta-filter -q will only discard alignments that are fully contained by a
better alignment on the query. Alignments that overlap, but each contain
some unique sequence, will be kept.

-Adam


On Tue, Nov 3, 2015 at 3:31 PM, Afif Elghraoui <ael...@sd...> wrote:

> Hi, Adam,
>
> On 11/03/2015 12:05 PM, Adam Phillippy wrote:
>
> Nucmer alignments will often overlap for the same reason MUMs can overlap
> (repeats). In the example you give the alignments overlap on the reference,
> but they do not overlap on the query. delta-filter -q tries to find the
> best alignments that cover as much of the query sequence as possible. Thus,
> this little 714 bp sequence appears duplicated in your query, but not your
> reference. delta-filter keeps it because it explains positions 3744105-3744818
> on the query.
>
>
> I understood that one, but I was referring to the middle line. Here is the
> snippet again:
>
> 3569553 3701911 3570622 *3702980* 132359  132359  99.99   4419977 4425991
> 2.99    2.99 ...
> 3701734 3741905 *3702919* 3743090 40172   40172   99.98   4419977 4425991
> 0.91    0.91 ...
> 3741192 3741905 3744105 3744818 714     714     98.60   4419977 4425991
> 0.02    0.02 ...
>
> The actual positions 3702919-3702980 in the query overlap in the first and
> second lines. I understand why the alignment is overlapping, but shouldn't delta-filter
> -q have filtered out the alignment corresponding to the second line here?
> In other words, is delta-filter -q *supposed* to throw out all alignments
> that result in query overlaps?
>
>
> I promise you will find many similar examples as you continue to play with
> the data. These types of alignments are very common when aligning
> assemblies to references (due either to mis-assembly or true variants), and
> sorting them all out is a very difficult problem.
>
> Of course.
>
> Many thanks and regards
> Afif
>
>
>
>
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