Different somatic calls across Monopogen v.1.0 and v1.6.0

[ypershad]

We are following the example here and noticed the following overlap with the example data between somatic SNV calls made from scRNAseq with v1.0 and v1.6.

Are you surprised that ~25% of the variants differ between versions? Do you think that the v1.6 calls are more trustworthy?

Thanks for any input that you have and for building this wonderful tool.

[jinzhuangdou]

Thanks for you posting such comparison. Your testing is based on our chr20 MAESTER dataset or yourself? I will look at a bit and feedback to you soon.

[ypershad]

Based on your chr20 MAESTER dataset. Thank you!

[jan-engelmann]

Hey,
do you have an update here? 🙏

[jinzhuangdou]

Hi, could you try the new version (updated in Jun 23,2024)? Only running the LDrefinement step is okay. The current version v1.6.0 imposes more filtering than v1.0.1. In v1.0.1, I noticed there are some loci with multi-alleles. This leads to the inconsistence on sequencing depth counting. The new version has fixed this issue.

[jinzhuangdou]

Another is you can check whether the discordance loci between two versions are both low sequencing depth. The updated version is the optimal one.