Running numbat on merged bam [smart-seq] about numbat HOT 3 CLOSED

Hi @Laolga ,

This is not officially supported yet but to run --smartseq mode, you can supply a txt file containing directories of bam files to --bams and a file containing cell names to --barcodes (each entry on its own line for both files). The --samples argument can just be one sample name.

You can see how the arguments are passed to cellsnp-lite here:
https://github.com/kharchenkolab/numbat/blob/main/inst/bin/pileup_and_phase.R#L90-L105

https://cellsnp-lite.readthedocs.io/en/latest/manual.html#full-parameters

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Great! Thank you for the reply

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Hi @Laolga
Did you get past this issue? I dont have the exact same issue but something simliar. When I try to run the preprocessing script I get the error Error in value[[3L]](cond) : Pileup failed Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted

Have you any idea what would be causing this issue? thanks

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