Emit intervals to realign (exome) - Error GATK

[Mandor]

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 :

http://genome.ucsc.edu/cgi-bin/hgTab...a_outFileName=

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!,

[Zaag]

Check if your fasta also has chr1 and not just 1. If not, remove the chr from your intervals file and try again.

[Mandor]

Hello Zaag,

Thanks for your help, that's it!