Hello,
To generate interval file usign GATK is needed a .bed file to specify the positions of human exome (hg19) (let's say "all_captured_exomes.bed").
To get this file, I went to UCSC and specify certain parameters to get this .bed file. So, concretely :
And 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 :
Thanks for your time!,
To generate interval file usign GATK is needed a .bed file to specify the positions of human exome (hg19) (let's say "all_captured_exomes.bed").
To get this file, I went to UCSC and specify certain parameters to get this .bed file. So, concretely :
And 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 what could it be?Thanks for your time!,
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