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.
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Parimala Devi
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.
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karl.stamm
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.
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Parimala Devi
SAM files can be used if the alignments are sorted by start position and indexed
Does your file meet this.
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Sukhi Singh
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What kind of SAM file? Is it from a weird process or new technology?
I have SAM files from SOAP, RUM, BOWTIE2 and BWA.