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.
Get all VCF files in proper format?
I tried running the following command to generate the VCF file using Haplotype Caller
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller --dbsnp chr7.vcf -R chr7.fa -I chr7.bam -A AlleleBalance -stand_call_conf 30.0 -stand_emit_conf 10.0 -dt NONE --output_mode EMIT_VARIANTS_ONLY -nt 1 -filterMBQ -rf BadCigar -rf MappingQualityZero -rf BadMate -o test.vcf
However, the poutput files obtained are having issues in the Format column i.e. instead of getting values in GT:AD:DP:GQ:PL format for all the varaints it is giving me only GT in some and GT:GQ:PL in others. Now is there any way to provide an input so that the format is same for all variants i.e. even if there is no value for DP it gives me NA / 0 instead of not printing it at all.
This vcf file acts as a part of further down stream analysis for annotation purposes so I need it a specific format so that I can create a parser for the same.