HaplotypeCaller interval list
REQUIRED for all errors and issues:
a) GATK version used: 4.1.2.0
b) Exact command used:
"gatk --java-options -Xmx8G HaplotypeCaller \
-I "+un_fichier+" \
-R reference_genome/GRCh38_latest_genomic.fna \
-O ./vcfs/"+un_fichier+"_"+region+".g.vcf \
-ERC GVCF \
-L "+region+" \
--native-pair-hmm-threads 2 \
--min-pruning 0"
c) Entire program log:
A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chr14" is not valid for this input.
Hello, I am trying to call variants from several WGS BAM files I generated using the Homo_sapiens_assembly38.fasta reference genome provided in the gatk ressources.
My strategy is to generate gvcf per chromosome and then merge them into a single one in order to save time. However I always get this error :
"A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chr14" is not valid for this input."
the provided dict is formatted as follow
"@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens"
So I thought "chr1" would work.
I also tried "SN:chr1" but same error.
Any clue on how should I put this ?
Thanks
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Hello Leo, I met the same problem when I used the gatk HaplotypeCaller -- intervals command, it shows to me "A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chr16" is not valid for this input."
it's amazing~ I think my reference is complete and has the correct name, which should not appear. I have tried searching on the net and see that you have the same problem, but there is no solution.
I have tried multiple times and see that my .dict file shows that Chr16-21, ChrX, and ChrY are vacant, I went back and looked at my reference genome and this does exist, I just need to recat the complete genome and try again.You can refer to my experience, good luck.
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