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VSQR resource format: which elements of vcf are needed?
Dear GATK team,
I am working with maize aDNA and would like to find SNPs called in aDNA samples that are at least as good as those in HapMap.
Am right to assume that variant recalibration is the correct tool for the job? My problem is that I can't find details about format of "resources" used for training. (I would like to see your hapmap.vcf but i can't log in to your ftp; it tells me that there can be only 25 users there).
From your documentation (https://www.broadinstitute.org/gatk/guide/article?id=2805 ; https://www.broadinstitute.org/gatk/guide/article?id=1259 and https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php#--resource) I gather that the training set needs to be in vcf file.
Here is my question:
Which components are important in resource vcf file; positions? variants? annotations? are SNP calls for each individual important?
In other words, is the purpose of training "resource" to
1) find overlapping sites in my vcf and use annotations that are in my vcf or
2) is it the training resource annotations that are being used?
If the former is true, would it be possible to use bed files instead? If the latter is true, do I need individual calls? HapMap for my organism has > 1000 individuals and is very heavy; if possible I would like to avoid downloading it all.
Many thanks for your help,