... | ... | @@ -121,8 +121,8 @@ no SNPs in this list that are intergenic? |
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For some purposes, it might be more convenient to have the annotations
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directly in the VCF. You could for instance do the following:
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` gunzip -c BT18_rsnumbers.vcf.gz | perl /home/formacion/COMUNES/IAMZ/soft/ensembl-tools-release-78/scripts/variant_effect_predictor/variant_effect_predictor.pl --dir /home/formacion/COMUNES/IAMZ/data/CIHEAM/ReferenceGenome/VEP/ --species bos_taurus -o BT18.vep.vcf --fork 4 --canonical --sift b --coding_only --offline --force_overwrite --vcf `\
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` bgzip BT18.vep.vcf`\
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` gunzip -c BT18_rsnumbers.vcf.gz | perl /home/formacion/COMUNES/IAMZ/soft/ensembl-tools-release-78/scripts/variant_effect_predictor/variant_effect_predictor.pl --dir /home/formacion/COMUNES/IAMZ/data/CIHEAM/ReferenceGenome/VEP/ --species bos_taurus -o BT18.vep.vcf --fork 4 --canonical --sift b --coding_only --offline --force_overwrite --vcf `
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` bgzip BT18.vep.vcf`
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` tabix -p vcf BT18.vep.vcf.gz`
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Again, study and interpret your outcome by looking inside the file.
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