[AMOS-help] .aft to .sam conversion error

[Wes B. <wes...@cs...>]

I have run Velvet on a set of Illumina paired end reads.  The output of
Velvet is a .afg file.  I am using AMOS to convert this to SAMtools format.
Here are the steps that I used:

$amos/bank-transact -m velvet.afg -b velvet.bnk -c
$amos/bank2contig -s velvet.bnk > junk.sam

The sam file contains a number of reads with a start coordinate less
than 1 (one).  Here is one example:

3       0       3-0     -4      255     78M     *       0       0       AAAACGAG
GGAGGGGGAGAAAGGGGTGAGCGGAGGGGAGAATGGGTGTAACAGGGAAAGAGGTGGCGAGCAGAGAGAG  22224828
88288888282228888E828488288882822E888E8E22428882228288E884828428282828

A start coordinate less than 1 violates the SAM specification.  To fix
this I wrote a script to modify the SAM CIGAR string and to reset the
start coordinate to 1 so that the above line now looks like this:

3       0       3-0     1       255     5S73M   *       0       0       AAAACGAG
GGAGGGGGAGAAAGGGGTGAGCGGAGGGGAGAATGGGTGTAACAGGGAAAGAGGTGGCGAGCAGAGAGAG  22224828
88288888282228888E828488288882822E888E8E22428882228288E884828428282828

It seems to me that the "bank2contig" SAM converter should be fixed
to better handle reads with a negative start.
-- 
Wes Barris