bcl-convert and UMI's

Question

[matthias.desmet]

Hi,

We're looking into using bcl-convert as an alternative for Picard wrt "UMI aware" demultiplexing.

Picard can demultiplex straight to bam with the UMI in the correct RX tag. bcl-convert appends the UMI sequence to the fastq header line when using the OverrideCycles option.

I'm looking for a way to get the UMI sequence from the fastq header into the sam RX tag (with or without alignment). I've already looked into fgbio, umi-tools, umis; but none of these tools seem to be able to handle the output format from bcl-convert.

Does anyone have a suggestion?

Thanks M

[GenoMax]

none of these tools seem to be able to handle the output format from bcl-convert

Output from bcl-convert will be fastq files. Indexes can be in separate files if needed. Are you using a specific library kit?