when I followed the pipeline:
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
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
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