GenotypeGVCFs
Hello i am trying to Joint genotyping for all individual VCF samples using this code:
java -Xmx48g -jar $GATK_JAR GenotypeGVCFs -R /lustrehome/vincenzolandi/dati_genomici/reference/sheep_genome.fna --variant /lustrehome/vincenzolandi/sra/sra2/SRR16036513_g.vcf.gz --variant /lustrehome/vincenzolandi/sra/sra2/SRR16036511_g.vcf.gz --variant /lustrehome/vincenzolandi/sra/sra2/SRR16036510_g.vcf.gz -O 4samples.vcf
i am using GATK Version:4.5.0.0
the code give error "A USER ERROR has occurred: Illegal argument value: Argument 'V/variant' cannot be specified more than once." maybe this version not accept multiple --variant argumet? I found a tools "GatherVcfs" that shoud do this but i have no exprience...any suggestions?
thank you,
Vincenzo
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You need to collect all GVCF files using GenomicsDBImport or CombineGVCFs tool before running GenotypeGVCFs. If you don't have too many samples ( # < 50) at hand CombineGVCFs will do the job just fine.
https://gatk.broadinstitute.org/hc/en-us/articles/21905054376859-CombineGVCFs
https://gatk.broadinstitute.org/hc/en-us/articles/21905031525019-GenomicsDBImport
I hope this helps.
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Hi, thank you very much!I try the following:
"java -Xmx48g -jar $GATK_JAR CombineGVCFs -R /lustrehome/vincenzolandi/dati_genomici/reference/sheep_genome.fna --output 4samples.vcf --variant SRR16036513_g.vcf.gz --variant SRR16036511_g.vcf.gz --variant SRR16036510_g.vcf.gz --variant SRR16036508_g.vcf.gz" and it seem working but he say that it need the index of each file. Should i create it as follow: "java -Xmx4g -jar $GATK_JAR IndexFeatureFile -I SRR16036513_g.vcf.gz " or it means the reference sequence index?
thank in advance, regards
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Yes you are absolutely correct. Each variant file must be indexed.
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