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MuTect2 ->Reference name for '1283' not found in sequence dictionary

Hi, I am trying to runjava -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:
1. samtools faidx to create the ucsc.hg19.fasta.fai file
2. 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 ?
Answers
@t1000
Hi,
Can you post the BAM file header and the FASTA dict file here? Specifically, I need to see if the @SQ lines in the BAM file match the ones in your dict file.
Thanks,
Sheila
Hi,
I'm having a similar issue with MuTect2 (GATK version 4.0.3.0).
I'm trying to run:
And I'm getting this error, with a different number after reference name each time:
I've checked the @SQ lines of both the .dict file and the .bam files, but can't see any obvious differences. Here is my .dict file:
and here are the @SQ lines from the ${TUMOUR}.recal.bam file:
I did use samtools reheader to change something in the header of my ${NORMAL}.recal.bam file (not the @SQ lines), and I notice that in this topic a ReadGroup was added to the bam file. Could this be the issue?
Thanks,
Michael
@michaelmc
Hi Michael,
Can you confirm this happens with the latest version?
-Sheila
Yes, I've tried it with 4.0.8.0 and I get the same error
@michaelmc
Hi Michael,
Thanks. I need to ask the developer and get back to you.
-Sheila
EDIT: This has been resolved in this thread.