As reported here:
http://gatkforums.broadinstitute.org/discussion/comment/4114#Comment_4114
If you encounter this bug too, please don't post a new question about it. Feel free to comment in this thread to let us know you have also had the same problem.
Thank you for your patience while we work to fix this issue.
We have received reports of a bug occurring with HaplotypeCaller in v2.4, with the error message "Reads are too small for use in assembly." We are working to fix it.
In the meantime, if you encounter it too, please don't post a new discussion about it, but do post a comment on this announcement so that we can count how many people are affected.
Thank you for your patience and our apologies for the inconvenience!
Hi,
I used the UnifiedGenotyper (GATK 1.6) on a multi-sample set to call variants, and for some of the positions I get multiple mutated alleles. The genotype entries in the combined VCF file look like (GT:AD:DP:GQ:PL):
0/1:94,11,0:124:22.18:22,0,2485,209,2500,2709
0/2:27,0,54:81:99:1651,1726,2695,0,968,836
so it's three AD values per entry. Running SelectVariants yields the following line for the second example from above:
GT:AD:DP:GQ 0/1:27,0,54:81:99
Although it changed the genotype from 0/2 to 0/1, it did not update the AD field. I checked the forums, but I could not really find anything discussing specifically the update of AD, except for the GATK 2.2 release notes where it says SelectVariants: "Fixed bug where the AD field was not handled properly. We now strip the AD field out whenever the alleles change in the combined file."
I was wondering whether you could confirm if cases like the one above would benefit from the bugfix, or if the bug description applies to something else.
Thanks a lot for all your hard work, Markus
