Question: Reference allele is too long message GATK
0
gravatar for win
8 months ago by
win790
India
win790 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 • 345 views
ADD COMMENTlink modified 8 months ago by WouterDeCoster34k • written 8 months ago by win790
0
gravatar for WouterDeCoster
8 months ago by
Belgium
WouterDeCoster34k 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 8 months ago by WouterDeCoster34k

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 8 months ago by win790

And does that help for these errors?

ADD REPLYlink written 8 months ago by WouterDeCoster34k

No, thats the problem.

ADD REPLYlink written 8 months ago by win790

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

ADD REPLYlink written 8 months ago by WouterDeCoster34k

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

ADD REPLYlink modified 8 months ago • written 8 months ago by win790
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