The documentation for Samtools is minimal at best. I'm still confused on the concept of a clipped read.
- What is a clipped read? How is it different from a deletion?
- What is a Soft clip? If the sequence is present in the reference is it different from a mismatch?
- What is a Hard clip?
Say if I wanted to calculate base pair coverage, would I include soft clipped bases because 'they are present in the <seq>?'
If someone can provide an example such as
REF: AGTCG GATCG GTACG
Read: AGTCG xxxCG GTACG
That would be even more awesomeer
One last question:
I found a ' * ' as a CIGAR string, what does that mean?