If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
MuTect2 ->Reference name for '1283' not found in sequence dictionary
Hi, I am trying to run
java -jar GenomeAnalysisTK.jar -T MuTect2 -R ucsc.hg19.fasta -I:tumor tumor_rg.bam -I:normal normal_rg.bam -o output.vcf
I am using ucsc.hg19.fasta as a reference and I used:
samtools faidx to create the ucsc.hg19.fasta.fai file
java -jar picard.jar CreateSequenceDictionary REFERENCE=ucsc.hg19.fasta OUTPUT=ucsc.hg19.fasta.dict
I added a ReadGroup to my two BAM Files:
java -jar picard.jar AddOrReplaceReadGroups I=normal.bam O=normal_rg.bam RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20
I also validated the BAM files
Now I get the following error:
##### ERROR MESSAGE: SAM/BAM/CRAM file /analysis/tumnormalor.bam is malformed. Error details: Reference name for '1283' not found in sequence dictionary.
If I exchange the tumor and normal .bam files as command line arguments I get the error
##### ERROR MESSAGE: SAM/BAM/CRAM file /analysis/tumor.bam is malformed. Error details: Reference name for '1283' not found in sequence dictionary.
I tried to google it and found nothing. Can someone give me a clue where to look ?
Is the file
ucsc.hg19.fasta.dict the sequence dictionary ?