Bwa/Samtools Soft-Clipping To Retrieve Back Whole Read

Question

[2184687-1231-83-]

Hi,

(I've been googling for this and couldn't find the answer)

Am I right in thinking that the default bwa/samtools instructions in the website will hard-clip the reads in the SAM/BAM files?

In the usual pipeline for single fragment reads: bwa aln ... bwa samse ... samtools view ... samtools sort ... samtools index ...

How can I end up with a final SAM/BAM file that contains the whole of the read/qualscore even if it's not fully matched?

Cheers

[lh3]

No, it is soft clip.

Answer 1

[Ketil]

I've been using bwa, and I see soft-clipped reads in the results. I doubt that samtools will change this. As far as I can tell, the BAM files also contain the whole reads.