Dear All,
I have to call genotype for multiple samples using joint genotyping methedology of GATK best practices, So I made a shell script which take list of samples in a text file as an input, and script through all commands on each sample one by one up to GVCF step. After generating GVCF for each sample, I want to call joint genotype using following command:
java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R hg19.fa -V sample1.g.vcf -V sample2.g.vcf [.. -V sampleN.g.vcf] -o rawVariants.vcf
So I pass "-V sample1.g.vcf -V sample2.g.vcf -V sampleN.g.vcf" as a variable like below:
V="-V sample1.g.vcf -V sample2.g.vcf .. -V sampleN.g.vcf"
java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R hg19.fa `echo $V` -o rawVariants.vcf
OR
java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R hg19.fa $V -o rawVariants.vcf
I got "ERROR MESSAGE: Invalid argument value '-V sample1.g.vcf -V sample2.g.vcf .. -V sampleN.g.vcf'.
Please provide me some way to pass '-V sample1.g.vcf -V sample2.g.vcf .. -V sampleN.g.vcf' to the GATK command in shell script.
Thanks in advance!
Hi Hemant,
Both the syntax are correct and I am using it in similar way for years now. It should work in Ideal bash, (May be your version of bash behaving crazy).
However you can list all the vcf in plain text file (one file name per line) and then execute the as follows,
java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R hg19.fa -V VCF.list -o rawVariants.vcf
Revert back if it doesn't work for you.
Cheers!
Vivek
oh yes Vivek it works great! Thanks alot.
It may be some issue with BASH version, but with file with .list suffix it works fine.
BioStars thread can be found here: https://www.biostars.org/p/234378/#234394
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