Can zUMIs be used for DNA-seq data alignment?

[zhober]

Hi,

I have designed targeted primers and amplified specific DNA fragments using the Smart-seq3 pipeline, resulting in FASTQ files. Since DNA lacks splicing events, I am wondering if it is possible to use zUMIs for processing these data to obtain BAM files for variant calling.

Here are some specific questions:

Can zUMIs stop the workflow before the counting step?

Is it possible to omit the GTF annotation file when using zUMIs? Since DNA-seq does not involve transcripts.

How can I modify the STAR aligner parameters within zUMIs to better suit DNA-seq data? I assume certain RNA-seq-specific options (like handling splice junctions) should be disabled.