Error in indexing .bam files from STAR alignment using SAMtools
I have created sorted .bam files using STAR. I am trying to create .bai files using SAMtools1.14 I am able to index all but one of the files (generated at the same time with the same STAR command), but I get the following error:
samtools index: "file.bam" is in a format that cannot be usefully indexed
I am unclear as to why this is happening and what to do to fix the file so I can proceed.
• 4,200 views
•
link
updated
by
iamjli •
•
written
by
Elizabeth Alice •
•
written
by
Elizabeth Alice •
1 answer
Log in to answer this question.
More posts like this
-
samtools index: Numerical result out of range for both .bai and .csi
written by tnminh89 •
-
Can't create index file of Bam file
written by Zahed Alam •
-
samtools: Numerical result out of range
written by Gregor Rot
-
samtools mpileup fail to create bcf
written by mthm •
-
cant make index file for Wheat accepted_hits.bam file
written by meisam.radfar •
-
samtools index error
written by evelyn
-
Error while generating index files using samtools
written by bisht20diksha •
-
Changing n_lvls in htslib hts.c, or, samtools index error "Numerical result out of range"
written by A Soggy Waffle •
-
Samtools view does not recognize that I already have index file
written by gaiusjaugustus
-
I loaded a BAM (RNA-seq) file into IGV but cant see anything!
written by jyalda2 •
Can you run
samtools quickcheck -v your.bam?and
file file.bamI get:
when I run
samtools -v quickcheckWhat does this mean?
This error is given when you try to index a non-SAM, non-BAM and non-CRAM file, but it's a file that is a recognised data type. So maybe it's not actually a bam file?
Using "htsfile file.bam" will give you some clues as to what htslib believes the file contents to be. You can also try "samtools view file.bam" to see if it can even be displayed. If both check out then this is more interesting and pointing to an indexing issue, but I suspect you'll find something amiss before that.
You could also try doing "less file.bam" (or "zless file.bam" if it's gzipped) to visually inspect it incase something obvious leaps out.