Error in GATK HaplotypeCaller
I am getting the following error while running the following command:
gatk HaplotypeCaller --java-options '-Xms2g -Xmx31g -XX:ParallelGCThreads=4 -Djava.io.tmpdir=/u/rajeshpal93/scratch/ca/diva_test_final/temp/samtools' -R /ELS/els9/users/biosciences/references/ucsc/hg19/ucsc.hg19.fasta -I reads/recalibrated/DNA18-0067-R0001.dedup.recal.bam -O variant_calling/DNA18-0067-R0001.g.vcf.gz -ERC GVCF -L /ELS/els9/users/biosciences/references/ucsc/hg19/intervals/hg19_ncbi_refseq_sorted_merged.bed -ip 200 -G StandardAnnotation >& logs/gatk/HaplotypeCaller/DNA18-0067-R0001.genotype_info.log
the error
A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1_gl383516_fix given as location, but this contig isn't present in the Fasta sequence dictionary
I don't understand where is the problem. Is it the bam file or bed file?
Thanks in advance !!
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Hi, The error message is saying that there is a chromosome (in this case chr1_gl383516_fix) that is present in your input BAM (either in the header lines, or in the alignment, or both), that is not present in the genome fasta : ucsc.hg19.fasta you have provided. Check the header lines of your BAM using
samtools view -H my.bam(or alternatively don't use the -H param and grep on the output for chr1_gl383516_fix to find the source of error)On second thoughts, the BED file that you are providing is also worth checking. As a rule, given a standard BAM file, the sequence names in the header lines of that should match with all other sequence data inputs (genome fasta, BED file etc.)
Yess, found the culprit. It was the bed file indeed!! Thanks !!