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Illumina / strelka

Strelka2 germline and somatic small variant caller
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Problem with Strelka2's default parameter "maxIndelSize = 49" #194

Open Tinnaa opened 3 years ago

Tinnaa commented 3 years ago

Hi,

I have some data that contains long indels(>49bp) in bam files, if the maxIndelSize was set to 80, these indels would be called. I've always used the default parameter, but this will missing some indels(>49bp)，

I would like to know why Strelka2 set the default parameter of maxIndelSize to 49? And if I raise this parameter value, will it affect the other mutations ?

Looking forward to your reply.

Tinnaa commented 3 years ago

I have compared the maxIndelSize=80 and maxIndelSize=49, maxIndelSize=80 called out a few long indel (>49bp)，and some indels have slight difference in depth. I would like to know what is the original purpose of Strelka2 setting parameter maxIndelSize=49?

I'd appreciate any insight to this problem.