IGV does not show BAM file information
Hello I have analyzed RNA seq data from two samples. I have compared them for SNP discovery. First, I aligned the reads to a reference genome using HiSet and creating SAM files. SAM files were converted to BAM files that were piled up using samtools mpileup. Variants were called using bcftools call. Now i want to visualise the results. I use IGV. I have loaded the reference genome file, the VCF file and the two indexed BAM files. I can see the information on specific SNPs in the VCF file but, the BAM files, even though presented as a track in the IGV, shows zero coverage and do not show any reads. Please help
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what's the output of
in the region ?
Thank you for the quick response. The output is 0
Sorry, this is the full output:
You have to use your BAM file name and valid values for chrom, start and end. What was your exact command?
there is no read in that region.
Remember to zoom in significantly (start with a gene of your choice and go to that region) before you can start seeing actual reads.
Hi I am looking at a window of 275bp. I can see SNPs in the VCF file with coverage data but the BAM file coverage track say 0 coverage. When loading the BAM file to IGV, I get this error: Error encountered querying alignments: htsjdk.samtools.SAMException: Unexpected number of metadata chunks 3
what is the length of the LONGEST chromosome in your reference ? if it's greater than 2^32, then i won't be supported by IGV.