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LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Handling of soft-clipped bases #94

Closed rspreafico-vir closed 4 years ago

rspreafico-vir commented 4 years ago

Hi there

I am trying to confirm that soft-clipped bases are not used by LoFreq. I checked paper and documentation but couldn't find an answer. The motivation is to confirm that soft clipping primers from hundreds of overlapping amplicons (e.g. using primerclip) will truly hide the primer bases from LoFreq. Variant callers that use local realignment will rescue soft-clipped bases, but I believe LoFreq will not (which would be great for my use case).

Thanks Roberto

andreas-wilm commented 4 years ago

Hi Roberto,

LoFreq will ignore soft clipped bases. The viterbi realigner won't touch them either.

Best, Andreas

On Sun, 31 May 2020, 02:48 Roberto Spreafico, notifications@github.com wrote:

Hi there

I am trying to confirm that soft-clipped bases are not used by LoFreq. I checked paper and documentation but couldn't find an answer. The motivation is to confirm that soft clipping primers from hundreds of overlapping amplicons (e.g. using primerclip https://github.com/swiftbiosciences/primerclip) will truly hide bases from LoFreq. Variant callers that use local realignment will rescue soft-clipped bases, but I believe LoFreq will not (which would be great for my use case).

Thanks Roberto

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rspreafico-vir commented 4 years ago

Thanks for confirming @andreas-wilm !