Question: Reference allele is too long message GATK
0
gravatar for win
11 months ago by
win800
India
win800 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 • 441 views
ADD COMMENTlink modified 11 months ago by WouterDeCoster36k • written 11 months ago by win800
1
gravatar for WouterDeCoster
11 months ago by
Belgium
WouterDeCoster36k 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 11 months ago by WouterDeCoster36k

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 11 months ago by win800

And does that help for these errors?

ADD REPLYlink written 11 months ago by WouterDeCoster36k

No, thats the problem.

ADD REPLYlink written 11 months ago by win800

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

ADD REPLYlink written 11 months ago by WouterDeCoster36k

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

ADD REPLYlink modified 11 months ago • written 11 months ago by win800

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 6 weeks ago • written 6 weeks ago by Satyajeet Khare1.3k
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