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Badly formed genome loc: Contig 'chr1' does not match any contig in the GATK sequence dictionary
I hate to put this same error on the GATK forum again, but I went through many of these errors already posted on the forum, but none of the answers shed light on my issue.
I have my bam files aligned to GRCh37-lite and am using the same reference genome downloaded from ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests
I have next performed GATK best practices for pre-processing of these bams using the same ref genome without throwing any error in the process.
Currently I'm running MuTect as
java -Xmx56g -jar muTect-1.1.4.jar
And getting this error message:
ERROR MESSAGE: Badly formed genome loc: Contig 'chr1' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?
What more tests should I run to troubleshoot this issue?
Also, the interval list is what I created from a .bed file. I have restricted my bam files to a limited bed regions using the same file in a command "samtools view -@8 -b -h -L"
This was the file I was most confused about. Is it possible that this file is causing the error? First few lines of this file are:
Thanks a ton for your help!