which human genome reference does mixcr use?

[xiaoyu462]

Hi, I have the alignments.vdjca file with me, and I wish to know the human genome reference used by mixcr. I want to use IGV to view the read alignments to the reference. Thanks!

[mizraelson]

Hi, MiXCR uses its own reference which is based on the genome assembly. The version of the genome used to create the reference depends on the MiXCR version you are using. You can use our interactive library database to export the IGV reference sequences:
https://vdj.online/library

[xiaoyu462]

Thank you very much for the reply!

Then may I know how to convert the vdjca file into bam file for viewing on IGV?

And if there is a way to visualize the text file which is from running "exportAlignmentsPretty" on mixcr in IGV or other platforms?

My exported text or tsv files do not contain chr information. Will it be fine?

Thanks again!

[mizraelson]

You can't convert vdjca to bam directly as they are different formats. vdjca is a MiXCR-specific format designed for TCR/BCR genes alignments, while bam is a binary format for storing sequence data. However, you can use bam files as input for mixcr align. To extract data from a vdjca file, you have two options: exportAlignments and exportAlignmentsPretty. The fields available for exportAlignments can be found in the MiXCR documentation. MiXCR focuses on immune receptor gene analysis, which doesn't require chromosome information; therefore, chromosome (chr) information is not typically included in vdjca exports.