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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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can the somatic module identify indels? #66

Closed ad2n15 closed 3 weeks ago

ad2n15 commented 3 weeks ago

Thank you for developing this tool. I run the tool following somatic module, but I can not find any indels in the final somatic csv files. Do you have an explanation?

jinzhuangdou commented 3 weeks ago

Monopogen can identify INDELs in germline modules. However, the current motif-based search does not detect INDELs in the somatic module. If you already have candidate INDELs, you can check their sequencing depth in the ./germline/chr*.gl.vcf.DP4 file to verify their presence.

jinzhuangdou commented 3 weeks ago

We are planing to give an updated version to handle INDELs in somatic module soon.

ad2n15 commented 3 weeks ago

Thank you for your reply