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# WGS variant calling steps based on [GATK4 best practices](https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-) for germline short variant discovery
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by @mfpfox | this README is a TEMPLATE for future processing of individual germline WGS data (code specific to CAD12 processing shown in each of the following steps)
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Template for processing individual short-read germline WGS (code specific to ipsc line 'CAD12' shown)
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