How do I obtain vcf file in the BaseRecalibrator stage of the "Data pre-processing for variant discovery" protocol?
Data: Leave plant (non-human) tissue.
I am using GATK to obtain discovery of short variants for my Illumina HiSeq Xten based reads
for LEave plant cells. A reference genome is available.
I am at the "Data pre-processing for variant discovery" protocol.
Currently I have finished the MarkDuplicate stage (for my bwa mapped reads).
The next recommended stage is: BaseRecalibrator
However, BaseRecalibrator requires an input vcf file which I don't have yet at this stage of the "data pre-processing protocol?
After MarkDuplicate followed by sorting, I only have a sorted sam file with flags for duplications.
What am I missing here?
Thank you for your help,
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