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# HaplotypeCaller calling as heterozygotes incorrectly

Member Posts: 94

I am finding that HaplotypeCaller is calling heterozygotes when there is no evidence when you look in IGV. Is this still a known problem?

I am using version 2.8-1-g932cd3a. Attached are two screen shots in IGV where a heterozygotes is wrongly called:

Tagged:

It seems that it is still a problem, yes. Can you please upload a test snippet so we can debug locally?

Geraldine Van der Auwera, PhD

• Member Posts: 94

OK. I have uploaded the files (10 files called snippet_01.bam etc) to a New Folder in the FTP incoming section, with a file showing the command I used (command_used_mboursnell.txt. An example of the error is at 40060422

Great, thanks Mike. We'll have a look at this asap.

Geraldine Van der Auwera, PhD

Mike, can you tell me what is the name of the directory you created to upload your files? I can't seem to find them.

Geraldine Van der Auwera, PhD

• Member Posts: 94

I made a new directory, which it called New Folder, but I couldn't rename it (permssions). So it's in:

Hi @mike_boursnell, it looks like you uploaded this to the general Broad FTP, not our group's. What login credentials did you use? In future we do prefer if you use our FTP. (see http://www.broadinstitute.org/gatk/guide/tagged?tag=ftp)

Anyway, I've got your data, but could you please upload your reference as well? We only have human references, it looks like you're working with dog (canfam?), which we don't have on hand.

Geraldine Van der Auwera, PhD

• Member Posts: 94

Ah, fair enough. Thanks for the direct link, that works too.

Geraldine Van der Auwera, PhD

• Member Posts: 94
edited December 2013
• Member Posts: 94

Hi. Is the problem with Haplotype_Caller corrected in the new GATK v3. Thanks

Hi Mike,

I believe this issue is fixed, yes -- at least if you use the new reference model pipeline.

Geraldine Van der Auwera, PhD

• Member Posts: 94

OK - thanks. I'll give it a go....

• AustraliaMember Posts: 1

I have a few samples sequenced in duplicates to check the consistency of genotype calls with gatk. I found several discrepancies between the duplicate samples. Most of them are related homozygotes to heterozygotes. That is if a site is called homozygote in one sample the same site is called heterozygote in another sample of the duplicate pair. I tried several filters suggested in the forum but none of them seem to improve the calls. Using BAM files in IGV clearly show same genotype at a position in the two samples of the duplicates yet gatk calls are different. Could you please help.