Hi all,

I just had to analyze a really bad lane. It is an old Illumina GAIIx lane with reads of 152 cycles. The last 30-40 cycles are of really really bad quality on average so I decided to use the -q 20 switch in bwa aln to trim reads 3'ends based on quality prior to mapping (something I usually would not do).

To have a look at what this trimming parameter left in the BAM file I drew the distribution of the length of soft-clipped part in the reads. To do so, I took the CIGAR string for 20 million alignments that were declared unique by BWA (XT:A:U tag). Here follows what I got :

So we can see that there is a periodic pattern after the main pic (representing no soft-clipped bases). We can also notice the slightly higher bar at position 117. 152-117=35, indeed by default BWA won't trim the reads to something less than 35bp.

Have you already noticed such a pattern using bwa aln -q and what in the algorithm produces this ?

Because looking at the -q definition in the doc, I can not see any reason why the trimming would have such a periodic pattern.

Thanks guys.

T.