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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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Could not retrieve index file for .bam #119

Open nansne opened 3 months ago

nansne commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

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 ... 微信图片_20240318154326

hxj5 commented 3 months ago

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