BAM files

[pkerpedjiev]

Hey, it's really amazing that you made all this data available! I was just curious if you happened to have alignments (BAM or CRAM) to the latest v1.0 assembly?

[Rohit-Satyam]

Also, are the annotations available for this assembly?

[skoren]

I just added bam files for the assemblies of the relevant techs (HiFi, CLR, ONT, Illumina).

As for annotations, I expect liftover annotations will be available soon through UCSC soon.

[pkerpedjiev]

Thanks a bunch! At the risk of pushing my luck, you wouldn't happen to have index (.bai) files as well would you?

[skoren]

We do have bai files but I usually prefer not to post easily-regenerated data/files to avoid cluttering up the downloads too much. The bai should be possible to regenerate on your side by running samtools index, no? Let me know if that doesn't work for some reason.

[pkerpedjiev]

That makes sense, but even though the .bai files are easy to generate the process does require downloading the entire BAM files. That's a lot of data transfer to generate a small index file.

One potential solution would be to store them without explicitly linking to them. For example, if the BAM file is stored at:

s3://bucket/my.bam

Then the index file would be at:

s3://bucket/my.bam.bai

When I first saw the bam files, I almost instinctively checked for the bai files at those locations. It wouldn't clutter the output and it would save a lot of data transfer.

What do you think? If that's not a feasible suggestion, then I can just generate them myself.

[skoren]

OK, I added the bai files with the same names as the bam just with the bai afterwards. So there is

https://s3.amazonaws.com/nanopore-human-wgs/chm13/assemblies/alignments/chm13.draft_v0.9.clr.bam

and corresponding

https://s3.amazonaws.com/nanopore-human-wgs/chm13/assemblies/alignments/chm13.draft_v0.9.clr.bam.bai

[pkerpedjiev]

Woo hoo! Thank you Sergey!! You saved me a lot of downloading.

And in case you're curious, here's the reason I was asking: pretty pileups from https://resgen.io/viewer/CM7MAF6nTymyK92-ZLQZTw

[marcpaga]

Would it be possible to upload the bam files for v2.0?

[arangrhie]

We have all the bam files from CHM13 reads on v1.1, which is v2.0 except the chrY (note CHM13 doesn't have the Y, the Y here is from HG002): https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/alignments/.