PairHMM bug in HaplotypeCaller?
HaplotypeCaller gave after analyzing 20 % of a 173 Gb Bam file an error: "java.lang.IllegalStateException: Pair HMM Log Probalility cannot be greater than 0: haplotype (..a long list of numbers..), result: Infinity".
The Bam file as fixmated with Picard tools and BaseRecalibrated.
I used the dbSNP,vcf file from the bundle; -rf BadCigar and -nct 8 as settings (all the CPUs on the machine).
GATK 2.7.2 and Java 1.7.0_25.
I was asked by the program to present the forum with this (possible) bug.