GATK and IUB codes

[donorio.demeo]

Hello there,
i just registered to this great forum,
i'd like to ask my first question about Variant calling.

I am trying the new GATK Unified Genotyper module
for a whole exome experiment,
but one thing i cannot get from the output
(and which was available instead
in the MAQ SNP consensus caller i used before)
is the IUB codes for heterozigous SNPs.
GATK just give me the best alternative allele.

Does anybody here know how to get that information?
Thanks a lot!!

[donorio.demeo]

Hello there,
i just registered to this great forum,
i'd like to ask my first question about Variant calling.

I am trying the new GATK Unified Genotyper module
for a whole exome experiment,
but one thing i cannot get from the output
(and which was available instead
in the MAQ SNP consensus caller i used before)
is the IUB codes for heterozigous SNPs.
GATK just give me the best alternative allele.

Does anybody here know how to get that information?
Thanks a lot!!

I made a script to count every Base from the Samtools Pileup output.
Indeed the GATK read depth is always >= than the real information.