In Silico Fast.gz files for UMI data? (Unique Molecular Identifiers)
I need to create in silico reads for umi data. Is there any software out there? I need to create a non-consensus and consensus bam with known inputs to validate a pipeline.
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I just found this: https://gitlab.com/vincent-sater/umigen . UMI's add a level of complexity and cost to the experimental procedures. They are probably not widely used routinely outside of single-cell technologies like 10x.
What kind of data are you looking to simulate (WGS, WES, RNAseq)? What is the non-consensus/consensus referring to?
Somatic variants, rna-seq, WES, all sorts of stuff.
We use fgbio CallMolecularConsensus to call the consensus reads.