Hi! I'd like to create a PONs for Mutect2 using my...
# createpanelrefsa
Alba Méndez Alejandre
11/04/2025, 9:59 AMHi! I'd like to create a PONs for Mutect2 using my normal samples, but I can’t find whether it’s possible to use the fastq files instead of the bams. It seems as explained in the docs that it is only possible to pass the bam or cram. Thank you!
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Maxime Garcia
11/04/2025, 10:01 AMI am afraid it's only BAM or CRAM as input
Maxime Garcia
11/04/2025, 10:02 AMI'd recommend using #CGFUX04HZ for the preprocessing of your normal samples
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Alba Méndez Alejandre
11/04/2025, 10:04 AMGot it, thank you! I’ll use #CGFUX04HZ for the preprocessing then 😊
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Maxime Garcia
11/04/2025, 10:06 AMPlease let us know how it goes
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Rike Hanssen
11/04/2025, 10:55 AMquite a journey sarek -> createpanelrefs -> sarek again 😄
Rike Hanssen
11/04/2025, 10:56 AMdepending on how you want to set this up, maybe take a look at the
--step