Error in GATK HaplotypeCaller
0
0
Entering edit mode
3.8 years ago
Hyper_Odin ▴ 320

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 !!

alignment Assembly SNP genome • 1.6k views
ADD COMMENT
0
Entering edit mode

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)

ADD REPLY
1
Entering edit mode

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.)

ADD REPLY
0
Entering edit mode

Yess, found the culprit. It was the bed file indeed!! Thanks !!

ADD REPLY

Login before adding your answer.

Traffic: 1254 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6