Hi all,

The documentation for Samtools is minimal at best. I'm still confused on the concept of a clipped read.

1. What is a clipped read? How is it different from a deletion?
2. What is a Soft clip? If the sequence is present in the reference is it different from a mismatch?
3. 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 awesomer

One last question:

I found a ' * ' as a CIGAR string, what does that mean?

Thanks
Hard masked bases do not appear in the SEQ string, soft masked bases do.

So, if your cigar is: `10H10M10H` then the SEQ will only be 10 bases long.

if your cigar is `10S10M10S` then the SEQ and base-quals will be 30 bases long.

In the case of soft-masking, even though the SEQ is present, it is not used by variant callers and not displayed when you view your data in a viewer. In either case, masked bases should not be used in calculating coverage.

Both of these maskings are different from deletions. Masking simply means the part of the read can not be aligned to the genome (simplified, but a reasonable assumption for most cases, I think). A deletion means that a stretch of genome is not present in the sample and therefore not in the reads.

I'm not sure when H is used instead of the S and vice-versa. I would like to know that.