IGV can't view SAM file

Question

[Parimala Devi]

I'm trying to view SAM files I have got after alignment using IGV. When I try to load the SAM file I get the following error:

Could not initialize class org.broad.igv.sam.reader.AlignmentReaderFactory

The same error is encountered when I try using a BAM file.

[karl.stamm]

What kind of SAM file? Is it from a weird process or new technology?

[Parimala Devi]

I have SAM files from SOAP, RUM, BOWTIE2 and BWA.

Answer 1

[karl.stamm]

That sounds like IGV is broken, likely trying to read a broken SAM tile. Convert to coordinate sorted BAM and reindex; then update IGV to whatever version they're on now; it should work.

You can easily do these things with samtools.

[Parimala Devi]

I converted the file to BAM, sorted and indexed it all using samtools,again. Also, the IGV is in it's latest version v.2.0.30-1. I'm still getting the same error.

Answer 2

[Sukhi Singh]

SAM files can be used if the alignments are sorted by start position and indexed

Does your file meet this.