I have 11 bam files in total that are all being made into snap files with snaptools snap-pre. I followed the specifications for formatting the bam files (which are originally from CellRanger, but went through some processing), but am getting this error thrown:
`[E::idx_find_and_load] Could not retrieve index file for 'snapatac_input.bam''
This is the exact command that I am running:
snaptools snap-pre --input-file=snapatac_input.bam --output-snap=snapatac_output.snap --genome-name=hg38 --genome-size=hg38.chrom.sizes
Has anyone else faced a similar issue? Obviously, I am unable to index the bam files via samtools index because the bam files are sorted by read name and not position - that is why this issue has been stumping me so bad.
Hi all,
I have 11 bam files in total that are all being made into snap files with
snaptools snap-pre. I followed the specifications for formatting the bam files (which are originally from CellRanger, but went through some processing), but am getting this error thrown: `[E::idx_find_and_load] Could not retrieve index file for 'snapatac_input.bam''This is the exact command that I am running:
snaptools snap-pre --input-file=snapatac_input.bam --output-snap=snapatac_output.snap --genome-name=hg38 --genome-size=hg38.chrom.sizesHas anyone else faced a similar issue? Obviously, I am unable to index the bam files via
samtools indexbecause the bam files are sorted by read name and not position - that is why this issue has been stumping me so bad.Any help is appreciated!