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tamsen / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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How to call complex variants with Pisces? #19

Closed HEKntg closed 1 year ago

HEKntg commented 1 year ago

Hello, Pisces helps me a lot. Is there any option or any other tool for complex variants? Thank you.

tamsen commented 1 year ago

Hi there,

Thank you for using pisces! Scylla is a simple complex variant caller included in the pisces package (see wiki https://github.com/tamsen/Pisces/wiki and https://github.com/tamsen/Pisces/wiki/Scylla-5.2.10-Design-Document). Scylla can combine phased SNPs and indels into complex variants. You can use the -dist argument to specify the maximum allowable distance between the variants that can be phased.

best Tamsen

HEKntg commented 1 year ago

Hi, I'll try it! Thank you again!