insertions not seen

[Annie Cowell]

Hello,

I called indels using gatk's HaplotypeCaller, however in IGV I don't see some of the insertions that were called.  

I'm using igv version 2.3.65 and my alignment preferences are set to MQ 0 and I've tried removing all the filters.  

An example of this is attached.  In the vcf, the sample in the final column should have 9 reads with the insertion, however igv does not show an insertion at this position, as shown in the screen shot.

Thanks for the help,

Annie

[Jim Robinson]

IGV is just showing you what is in the BAM file, of course, it knows nothing about the VCF records.   I can't see all the reads here as some are scrolled out of view, and in any event  need access to these alignments to help further. You can extract them from the "right-click" track menu (select "Export Alignments".   This will create a SAM file with just the reads in view.   If you feel there should be insertions at a specific position center the view over this position, extract the reads, and I will send you a drop-box invitation where you may securely upload the SAM file.   If you're able to do this let me know.

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[Annie Cowell]

Hi Jim,

I was expecting to see a blue "I" indicating an insertion in this area, with the sequence shown when I hover over it as with other insertions. I right-clicked over the center line at the bp position where the insertion is called and exported the reads into a SAM file.

Annie

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[Jim Robinson]

OK, you should receive a dropbox request. If you don't see a blue "I"
it probably means its not there, but I will confirm that when I get the
SAM file.

[Jim Robinson]

If you have problems with dropbox you can also email the SAM file to      igv-...@broadinstitute.org.

Hi Jim,

I was expecting to see a blue "I" indicating an insertion in this area, with the sequence shown when I hover over it as with other insertions. I right-clicked over the center line at the bp position where the insertion is called and exported the reads into a SAM file.

Annie

s.google.com/d/optout.

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[Jim Robinson]

Got the file. There are no insertions in any of the reads in this file (I checked all cigar strings).

[Annie Cowell]

Must be an issue with the insertion call, I will check with the gatk folks. Thank you!  

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