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#!/bin/bash | |
## Download the HG002 30X VCFs shared by google | |
gsutil cp gs://brain-genomics-public/research/sequencing/grch38/vcf/novaseq/wgs_pcr_free/30x/HG002.novaseq.pcr-free.30x.deepvariant-v1.0.grch38.vcf.gz . | |
## Split multi allelics using bcftools norm | |
## (Assumes bcftools is installed and in your PATH) | |
bcftools norm -m- -Oz --output HG002.novaseq.pcr-free.30x.deepvariant-v1.0.grch38.split.vcf.gz HG002.novaseq.pcr-free.30x.deepvariant-v1.0.grch38.vcf.gz | |
## Tabix index our VCF file |