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Yes, that's what it means. Do you know of any tools that can query this file? The limitation is imposed by the BAM index format (see here (page 13): https://samtools.github.io/hts-specs/SAMv1.pdf. If you know of a tool that can successfully read and query this file in regions > 2^29 please let me know. It's a known limitation of the BAM format.
On Fri, Mar 10, 2017 at 4:28 AM, Mar <mara....@gmail.com> wrote:
I attach the igv.log
Il giorno venerdì 10 marzo 2017 12:20:51 UTC, Mar ha scritto:IGV version 2.3.90 (143)
When I try to load my bam file into IGV (the reference genome being already loaded), i get the following error:
Error loading SAM header: Sequence lengths > 2^29-1 are not supported
My reference chromosome genome (with wich the alignment was originally generated) is 779mb, does this mean that my index is too long for display?
P.s. the bam file was sorted and indexed (both in .bai and .csi format) using samtools:
samtools sort SNP.alignment.bam SNP.alignment.sorted
samtools index SNP.alignment.sorted (or samtools index -c for .csi)
Thanks in advance!
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