Question: Reference allele is too long message GATK
0
gravatar for win
2.5 years ago by
win840
India
win840 wrote:

hi all, i generated a gVCF file using HaplotypeCaller. When i run ValidateVariants from GATK i get the message

"Reference allele is too long (108) at position chr9:99423855; skipping that record. Set --reference_window_stop >= 108"

Any ideas what is causing this?

Command used to generate the gVCF

java -Xmx16g -jar algorithms/gatk3/gatk3.8.jar -T HaplotypeCaller -R references/hg38gatkbundle/Homo_sapiens_assembly38.fasta -I data/HG100/HG100.output.bam --emitRefConfidence GVCF --dbsnp references/hg38gatkbundle/Homo_sapiens_assembly38.dbsnp138.vcf -o data/HG100/HG100.output.raw.snps.indels.g.vcf --reference_window_stop 1000

Command used for validation

java -jar algorithms/gatk3/gatk3.8.jar -T ValidateVariants -R references/hg38gatkbundle/Homo_sapiens_assembly38.fasta -V data/HG100/HG100.output.raw.snps.indels.g.vcf --dbsnp references/hg38gatkndle/Homo_sapiens_assembly38.dbsnp138.vcf --validationTypeToExclude ALLELES

Any help highly appreciated.

vcf • 1.0k views
ADD COMMENTlink modified 2.5 years ago by WouterDeCoster44k • written 2.5 years ago by win840
1
gravatar for WouterDeCoster
2.5 years ago by
Belgium
WouterDeCoster44k wrote:

My guess is a long deletion, with 108 nucleotides in your reference allele field. As suggested by the error message setting --reference_window_stop to a value >= 108 should work.

ADD COMMENTlink written 2.5 years ago by WouterDeCoster44k

OK, but there are other such messages as well, same message but differing length like some say 108, some are 150 etc. I have also set --reference_window_stop to 1000.

ADD REPLYlink written 2.5 years ago by win840

And does that help for these errors?

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k

No, thats the problem.

ADD REPLYlink written 2.5 years ago by win840

Then, what error messages do you get with --reference_window_stop 1000?

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k

same message, it seems like the --reference_window_stop is not working or has incorrect values.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by win840

This worked fine for me.

java -jar  GenomeAnalysisTK.jar -T ValidateVariants --reference_window_stop >= 300 -R Genome.fa --variant:VCF All.vcf.gz
ADD REPLYlink modified 20 months ago • written 20 months ago by Satyajeet Khare1.5k
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