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***rule:** add GATK's HaplotypeCaller and filtering ([497180e](https://github.com/fcaretti/SNPs_from_RNA/commit/497180ec51338c9fab19498f895d4c421e0af3d8))
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***rule:** add index and dict to reference genome ([8022eb9](https://github.com/fcaretti/SNPs_from_RNA/commit/8022eb9dce48da04fe5d41a1536b0e112d43e02c))
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***rule:** add Split N CIGAR rule ([b2b38bb](https://github.com/fcaretti/SNPs_from_RNA/commit/b2b38bb7450159dd2934cea1d74dda3481b2faac))
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***rule:** add VEP annotation (no wrapper) ([2c72e6d](https://github.com/fcaretti/SNPs_from_RNA/commit/2c72e6dc2d2d6537df13c011e75753721e0db754))
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### Bug Fixes
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***main:** add bai file to output of BQSR ([c3bd9bf](https://github.com/fcaretti/SNPs_from_RNA/commit/c3bd9bfd2f9ce9024708b86087b81657dfcb5edf))
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***PR:** correct PR title ([8a3a321](https://github.com/fcaretti/SNPs_from_RNA/commit/8a3a3210389611295f399085c1dcfdc7f9f7e1e8))
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