GATK IndelGenotyperV2 ERROR

[wanguan2000]

when I followed the pipeline:

http://www.broadinstitute.org/gsa/wiki/index.php/Whole_exome_v1

java -Xmx4g -jar GenomeAnalysisTK.jar \
-l INFO \
-nt 8 \
-R ./hg19fasta/ucsc.hg19.fasta \
-B:dbsnp,vcf /share/user_data/wfz1/database/hg19database/dbsnp_132.hg19.vcf \
-I ./hg19fasta/pair-end32.sorted.bam \
-T CountCovariates \
-cov ReadGroupCovariate \
-cov QualityScoreCovariate \
-cov CycleCovariate \
-cov DinucCovariate \
-recalFile ./hg19fasta/32.csv \
--default_read_group HWI-ST499:5:5:8126:176904#CTTGTA \
--default_platform illumina

.......
in this step:

java -Xmx4g -jar GenomeAnalysisTK.jar \
-T IndelGenotyperV2 \
-l INFO \
-R ./hg19fasta/ucsc.hg19.fasta \
-I ./hg19fasta/cleaned31.bam \
-bed my.brief.output.bed \
-o my.detailed.output.vcf

I got this ERROR:
Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 1 is less than start 150
what is problem? I'm just following the pipeline.
ps:my bam data is : pair-end31.sorted.bam

[wanguan2000]

java -Xmx4g -jar /share/user_data/wfz1/wangguan/GATK/GenomeAnalysisTK-1.1-3-g1f8fc4a/GenomeAnalysisTK.jar \
-T SomaticIndelDetector \
-l INFO \
-R ./hg19fasta/ucsc.hg19.fasta \
-I ./hg19fasta/cleaned31.bam \
-bed ./hg19fasta/my.brief.output31.bed\
-verbose ./hg19fasta/my.detailed.output31.txt \
-o ./hg19fasta/my.output31.vcf

GenomeAnalysisTK-1.1-3-g1f8fc4a don't contain the IndelGenotyperV2, It has the SomaticIndelDetector.
in my case, the pair-end data was merger in one pair-end31.sam. The SomaticIndelDetector was need -I:normal data1.bam -I:tumor data2.bam.
what can I do?

[RDW]

'Paired sample mode' in the Somatic Indel Detector docs refers to tumour/normal pairs. If you don't have these, you can follow the instructions for 'Single Sample Mode' (the single input bam file can contain paired end data). However, in this case you'd be much better off following the current pipeline:

http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v2

This uses the Unified Genotyper to call both indels and SNPs. For help with this, see:

http://getsatisfaction.com/gsa

The old v1 pipeline you were using is not designed to work with recent versions of the GATK.