We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

HaplotypeCaller: Warning on no. of alternate alleles, and no output

rburrirburri Member
edited August 2012 in Ask the GATK team

Hi,

I am trying to run HaplotypeCaller (v2.1-2). So far I either encounter the problem concerning duplicate alleles already reported in the forum, or when this seems not to be a problem, I get the following warnings printed in the standard output:

WARN 12:45:23,436 ExactAFCalculationModel - this tool is currently set to genotype at most 3 alternate alleles in a given context, but the context at S00001:2508 has 5 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
WARN 12:51:42,119 ExactAFCalculationModel - this tool is currently set to genotype at most 3 alternate alleles in a given context, but the context at S00001:6359 has 6 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
WARN 12:58:56,899 ExactAFCalculationModel - this tool is currently set to genotype at most 3 alternate alleles in a given context, but the context at S00001:9252 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
WARN 13:03:12,906 ExactAFCalculationModel - this tool is currently set to genotype at most 3 alternate alleles in a given context, but the context at S00001:10748 has 4 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
WARN 13:05:22,546 ExactAFCalculationModel - this tool is currently set to genotype at most 3 alternate alleles in a given context, but the context at S00001:11028 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument

At the same time, nothing is printed to the specified output files.

I used the same files to call variants using UnifiedGenotyper, and this worked out well.

Thanks a lot for your help & best wishes,
Reto

Best Answer

Answers

Sign In or Register to comment.