Dear community members,
I got a CRAM aligned to a very customised reference with weird (not even "canonical" alt) contigs. They are not covered except several accidental reads and I can safely filter them out. Is there a way to do it for CRAM (I don't have this custom reference)? I know how to do it with BAM, but not sure if it will work with CRAM...
Perhaps you can create a dummy reference containing N's for the weird contigs (while matching the lengths).
Then use the valid sequences for the contigs you want to keep - if I read it correctly you have the main contigs - only the weird-ALTs are missing
then use that dummy reference to filter the CRAM file by the desired contigs.
indeed bioinformatics is more about how to work around the endless foundational problems or as Brent Pedersen put it 10 years ago:
I've been doing bioinformatics for about 10 years now. I used to joke with a friend of mine that most of our work was converting between file formats. We don't joke about that anymore.
10+10, makes the sentiment 20 year old now, and still applies just as much
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
I'm not sure you can do much things with a CRAM without reference...