Hello,
To generate interval file usign GATK little faster, I try to add the use the -L parameter for the walker "-T RealignerTargetCreator". This file, is a .bed file that specify the exome positions of human exome (hg19).
To get this file (let's say "all_captured_exomes.bed"), I went to UCSC :
It seems ok, but when I try to launch the aligner .... :
java -jar $GATK_HOME/GenomeAnalysisTK.jar -T RealignerTargetCreator \
-R /home/armand/mnt/cubix/Genomes/index/index/hg19/bwa_path/Homo_sapiens_assembly19.fasta \
-I $1 -log intervals.log -B:dbsnp,vcf $dbSNP \
-L ../exome_hg19_captured/all_captured_exomes.bed -o "$core_dir/${core_name}.intervals"
It gives me this error :
##### ERROR MESSAGE: File associated with name ../ref_gen_hg19/exome_hg19_captured/all_captured_exomes.bed is malformed: Interval file could not be parsed in either format. caused by Invalid command line: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary
Any ideas about this error?
Thanks for your time!,
To generate interval file usign GATK little faster, I try to add the use the -L parameter for the walker "-T RealignerTargetCreator". This file, is a .bed file that specify the exome positions of human exome (hg19).
To get this file (let's say "all_captured_exomes.bed"), I went to UCSC :
It seems ok, but when I try to launch the aligner .... :
java -jar $GATK_HOME/GenomeAnalysisTK.jar -T RealignerTargetCreator \
-R /home/armand/mnt/cubix/Genomes/index/index/hg19/bwa_path/Homo_sapiens_assembly19.fasta \
-I $1 -log intervals.log -B:dbsnp,vcf $dbSNP \
-L ../exome_hg19_captured/all_captured_exomes.bed -o "$core_dir/${core_name}.intervals"
It gives me this error :
##### ERROR MESSAGE: File associated with name ../ref_gen_hg19/exome_hg19_captured/all_captured_exomes.bed is malformed: Interval file could not be parsed in either format. caused by Invalid command line: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary
Any ideas about this error?
Thanks for your time!,
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