Variant annotation tutorial

Slicing and dicing of VCF files

 tabix -h allbt.vcf.gz 18 >BT18.vcf
 tabix -p vcf BT18.vcf.gz

Annotating VCF with rs-numbers

 tabix -h BT18.vcf.gz 18:100000-101000 | vcf-annotate -a BT_incl_cons.18.vcf.gz -c CHROM,FROM,ID

Extracting variants using BEDtools

select a region of BT18 with genes:

gunzip -c Bos_taurus.UMD3.1.78.gtf.gz | awk '$3=="gene"' | awk '$1==18&&$4>1000000&&$4<2000000'

bedtools intersect -a BT18.vcf.gz -b mygenes.gtf | more

Variant Effect Predictor

 gunzip -c /home/formacion/COMUNES/IAMZ/data/CIHEAM/MULTISAMPLE_VCF/all.fb.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 test2.vep --fork 4 --canonical --sift b --coding_only --no_intergenic --offline --force_overwrite --vcf