Fail to generate .bai index with samtools

Question

[bing.bai]

I am using

samtools index -b A.bam

to generate .bai indx file but I always get A.csi format index file.

Anything wrong with it?

[Ram]

What's your samtools version? I went through all of samtools versions, none of them produce csi files unless asked for with the -c parameter. Maybe there's an alias interfering with your command?

Also, even if you got the csi file, it should be A.bam.csi, not A.csi. Are you sure the csi file is being produced by the samtools command you're running?

[bing.bai]

yes, it's A.bam.csi, Here is the version Program: samtools (Tools for alignments in the SAM format) Version: 1.7 (using htslib 1.7-2) Here is the exact command I used

samtools index -b bai_R1_trimmed20-3.bam -m 18

I got bai_R1_trimmed20-3.bam.csi

[GenoMax]

Are you using a very large genome for these alignments? What happens if you don't use -m 18? Setting that may be leading to .csi indexes.

[bing.bai]

really? I use that cause I have large dataset to process. Will try without.

Answer 1

[GenoMax]

If you meant to use more threads (cores) then that option is -@ INT Sets the number of threads [none].

e.g. samtools index -@ 12 -b bai_R1_trimmed20-3.bam

[bing.bai]

Nice, it works. indeed -m has an effect on the output format. don't know why though;). Thanks.

[GenoMax]

By using -m you indirectly instructed samtools to create .csi indexes, since that option only applies to those.

[finswimmer]

Hello bing.bai ,

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