Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
ERROR MESSAGE: The provided VCF file is malformed
I have whole genome data for around 500 individuals for which I am running the GATK variant calling pipeline. I have run the exact same pipeline before on a much smaller data set and didn't experience any problems. Thus I am not sure what causes the problem described below and I hope you can provide me with some help on this issue.
Here is a short description of what I have done:
After all the data pre-processing steps, I have run GATK's HaplotypeCaller on each sample's bam-file using the following command:
"java -Xmx4g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R reference.fasta -I sample.bam --genotyping_mode DISCOVERY
--emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o sample.gvcf"
As suggested in the Best Practice Guide, I combined multiple gvcf-files using the following command:
"java -Xmx50g -jar GenomeAnalysisTK.jar -T CombineGVCFs -R reference.fasta --variant sample1.gvcf --variant sample2.gvcf (...) -o combined.gvcf".
This step runs through without any problem for all my samples but when I am trying to genotype them using
"java -Xmx100g -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R reference.fasta --variant combined1.gvcf --variant combined2.gvcf (...)
GATK throws the following error message: "ERROR MESSAGE: The provided VCF file is malformed at approximately line number 86995422: ./.:0:0:0:0,0,0 is not a valid start position in the VCF format"
Thank you in advance for your help!