Error loading cram file in IGV v2.11.9

[Matthias Habjan]

Hi there,

just started using IGV, and not yet been so successful in loading tracks. As a start, I have downloaded a cram and corresponding index file from the 1000 genomes project and loaded it as track to the GRCh38 genome.

It loads OK, but when I zoom in I get the following error message:

Error querying alignments for: HG01879.alt_bwamem_GRCh38DH.20150826.ACB.exome.cram
Error message: null     

Does anyone have an idea why this does not work?

I tried using the IGV web application with the same files. Then I get the following error message:

crc mismatch in container header beginning at position 2612092285: recordd CRC32 = 0, but calculated CRC32 = 2077607535

Appreciate your help,
Matthias

[igv-help]

Can you send us the URL to these files?

Helga

[igv-help]

The 1000 genome cram files were not aligned to the hg38 fasta IGV uses by default.  They should be viewed against the reference  with the tag. "hg38 GATK/1kg".    For many regions they will work, but for some you will get the CRC error because the reference they were aligned against do not match the reference you are viewing against.  

In general, for CRAM files,  you must use the exact fasta the CRAM was aligned to.   This of course is often difficult to obtain.

RE the "null" error you encountered in IGV desktop,  could you let us know the exact genome region where that occured?  I will look into improving the error message for that case.

[Matthias Habjan]

Hi Helga,

thanks for your reply. The URL to the files is as follows:

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/ACB/HG01879/exome_alignment/

I get the same error message when viewing against the "hg38 1kg/GATK". 

The error message comes for any region that I zoom into. But one example would be: chr14:73,512,743-73,530,326

[James Robinson]

I do not get any errors with that file at the locus provided (chr14:73,512,743-73,530,326),  see screenshot below.   Perhaps there is some network or firewall issue at your location?   Are there any errors in your igv log file (in the "igv" folder in your home directory, it might be named either igv.log, or igv0.log).

I'm also able to load at igv.org/app, note that https protocol must be used at https://igv.org/app.    Here is a shared url:   https://tinyurl.com/yabbstwt.