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

snpEff

== Inferring function

from VEP output to Polyphen/Provean input

extracting fasta record.

faOneRecord Bos_taurus.UMD3.1.pep.all.fa `cat Bos_taurus.UMD3.1.pep.all.fa | grep ENSBTAT00000063226 | awk '{print $1}' | sed 's/>//'`

Provean

>ENSSSCP00000018263 pep:novel chromosome:Sscrofa10.2:12:6621092:6624938:1 gene:ENSSSCG00000017236 transcript:ENSSSCT00000018765 gene_biotype:protein_coding transcript_biotype:protein_coding MTPRVGAVWLPSALLLLRVPGCLSLSGPPTAMGTKGGSLSVQCRYEEEYIDDKKYWDKSP CFLSWKHIVETTESAREVRRGRVSIRDDPANLTFTVTLERLTEEDAGTYCCGITAQFSVD PTHEVEVVVFPALGTSRPPSMPGPPTTLPATTWSFVSERETMANNLGKGPASQDPGQHPR SKHPSIRLLLLVFLEVPLFLGMLGAVLWVHRPLRSSESRSVAMDPVPGNTAPSAGWK

235,G,E 5,V,A 22,C,Y 34,T,I 51,D,N 53,K,N 59,S,Y 61,C,R 64,S,L 67,H,P 68,I,T 75,A,V 108,T,K 115,A,T 124,E,D 130,F,Y 133,L,P 142,P,A 155,F,I 158,E,G 186,I,V 21,G,D

1. 1. PROVEAN scores ##
2. VARIATION SCORE

235,G,E 0.076 5,V,A 0.287 22,C,Y -8.028 34,T,I -1.932 51,D,N -1.613 53,K,N 1.565 59,S,Y -2.140 61,C,R -5.826 64,S,L -0.437 67,H,P -0.511 68,I,T -2.664 75,A,V -1.061 108,T,K -4.051 115,A,T 1.557 124,E,D -1.587 130,F,Y -0.983 133,L,P 3.203 142,P,A -2.058 155,F,I 0.502 158,E,G -0.077 186,I,V 0.220 21,G,D -6.014