Could not retrieve index file for .bam

[nansne]

Hi,
I ran cellsnp-lite, and failed with "[E::idx_find_and_load] Could not retrieve index file for './gex_possorted_bam.bam'", so what should i do next?
Thank you very much!

[hxj5]

Hi, it seems the BAM index file is missing. You may use samtools index to generate the file, i.e.,

samtools index ./gex_possorted_bam.bam

It should produce ./gex_possorted_bam.bam.bai or ./gex_possorted_bam.bam.csi file.

[nansne]

thank you, so i put 'gex_possorted_bam.bam' and 'gex_possorted_bam.bam.bai' into the same folder, and run again, but it failed with ...

[hxj5]

Hi, the BAM file may be corrupted. To check the file, please see the comments on issue 32.