According to the suggestions raised by users of pTuneos and the update of the built-in software in our workflow, We have made some modifications to our tool to make it more comprehensive and easy to use.
The update include:
- pTuneos did not support indel neoantigen very well in VCF mode as we did not test it thoroughly in the first version, In the version 2.0.1, the neoantigen derived from SNV and INDEL can both be predicted correctly.
- In the WES mode of version 1.0, pTuneos utilized GATK mutect2 to call SNV and strelka to detect INDEL for neoantigen identification, in this version, only GATK mutect2 was retained for both SNV and INDEL detection.
- In the WES mode of version 1.0, pTuneos utilized varscan2 + sequenza v2.0 to calculate the copynumber profile of tumor sample, in this version, pTuneos only uses sequenza v3.0 to finish this step just taking bam file as input, thus varscan2 was removed from our pipeline.
- In this version, both SNV and INDEL derived neoantigens were saved together in a single file named "final_neo_mode.tsv".
- The docker version has been released.