Question: When Hard clipping is used instead of the Soft clipping ?
gravatar for 2012secondseason
2.7 years ago by
2012secondseason30 wrote:

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

I know that there are many explanations here that soft clipped bases are present in SEQ unlike hard clipped bases. But it's insufficient. In what cases, use H instead of S ??


hard clipping cigar clipping • 2.0k views
ADD COMMENTlink modified 2.7 years ago by Devon Ryan98k • written 2.7 years ago by 2012secondseason30
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

in bwa, HARD clipping is used for supplementary reads.

Information (full read sequence) is still available in the primary alignment.

ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum133k
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

This is purely up to the program creating the file, which is why this isn't described in the samtools documentation. A good example of a time when most programs would hard-clip a read is if they remove known adapter sequence. It's then not worthwhile including that sequence in the output. One could also think of hard-clipping regions when they're part of supplemental alignments (I've seen both hard and soft-clipping for that, though the former is probably more useful).

ADD COMMENTlink written 2.7 years ago by Devon Ryan98k

2012secondseason, for example, BWA mem gives you some control how you'd like to have the clipped sequences represented - you can toggle between soft and hard clipping using the -Y option. There used to be an option to remove soft clipping altogether, but that seems to have changed its meaning (at least comparing the online manual to the command line description)

ADD REPLYlink written 2.7 years ago by Carambakaracho2.3k
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