Badly formed genome loc: Contig chr1-10002766-10002840-10003307-10003381 given as location, but this

hello,

GATK: v2.7-4-g6f46d11

I get this error after RealignerTargetCreator (and using the UnifiedGenotyper):

"Badly formed genome loc: Contig chr1-10002766-10002840-10003307-10003381 given as location, but this contig isn't present in the Fasta sequence dictionary"

my complete call is:
java -jar GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-R $reference \
-I $BAM \
--filter_reads_with_N_cigar \
-known $indels \
-o $out/target_intervals.list

i use RNA-seq data, and mapped against the genome and an artificial exon-exon-junction database. coordinates from reads mapping against these junctions were back-translated to the genome afterwards (following the pipeline from: http://www.ncbi.nlm.nih.gov/pubmed/?term=24075185)

the bam-file seems to be correct...

chr1 is of course in the fasta-dict.
@SQ SN:chr1 LN:249250621 UR:file:/home/ws/SW_install/SNPiR/SNPiR/junctions/hg19.fasta M5:1b22b98cdeb4a9304cb5d48026a85128

or does "chr1-10002766-10002840-10003307-10003381" means something different?

thank you in advance for your help,

dietmar

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