When Hard clipping is used instead of the Soft clipping ?

Question: When Hard clipping is used instead of the Soft clipping ?

2.7 years ago by

2012secondseason • 30

2012secondseason • 30 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 ??

Thanks.

hard clipping cigar clipping • 2.0k views

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modified 2.7 years ago by Devon Ryan ♦ 98k • written 2.7 years ago by 2012secondseason • 30

2.7 years ago by

Pierre Lindenbaum ♦ 133k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 133k wrote:

in bwa, HARD clipping is used for supplementary reads.

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

ADD COMMENT • link written 2.7 years ago by Pierre Lindenbaum ♦ 133k

2.7 years ago by

Devon Ryan ♦ 98k

Freiburg, Germany

Devon Ryan ♦ 98k 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 COMMENT • link written 2.7 years ago by Devon Ryan ♦ 98k

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 REPLY • link written 2.7 years ago by Carambakaracho • 2.3k

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