Created
October 27, 2020 17:17
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bcftools csq and vcfanno to avoid vep
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| set -oexu pipefail | |
| VCF=$1 | |
| bcftools csq \ | |
| -f /scratch/ucgd/lustre/work/u0691312/reference/ucgd_reference/GRCh38/human_g1k_v38_decoy_phix.fasta \ | |
| -g /scratch/ucgd/lustre/work/u0691312/reference/Homo_sapiens.GRCh38.100.gff3.gz \ | |
| $VCF \ | |
| | vcfanno -p 12 \ | |
| /scratch/ucgd/lustre/work/u0691312/reference/vcfanno_revel.toml \ | |
| /dev/stdin |
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