10x VDJ (TCR/BCR) BAM to fastq

Question

[predeus]

Dear all,

I was wondering if anyone came across a tool that would correctly extract reads from all_contigs.bam file generated by 10x VDJ pipeline? Official bamtofastq does not support these files, but they are often the only thing that is available from GEO/SRA.

Thank you in advance,

-- Alex

Answer 1

[GenoMax]

Looking at the information about the BAM file in the link included at the end of this sentence, it seems that the BAM file does not contain all the data and you would not be able to recreate the entire starting dataset : https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-5p-outputs-bam-vdj