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

 gunzip -c test2.vep.vcf.gz | grep deleterious | sed 's/;/\t/g' | awk '{gsub("AF=","",$11); print}' | awk '$11<0.15&&$11>0' | wc -l

snpEff

 java -Xmx4G -jar $snpEff -dataDir ~/snpEff/data -v UMD3.1.78 sample_Bt.vcf >testresult_Bt.txt

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/>//'`

Polyphen

 /lustre/nobackup/WUR/ABGC/shared/public_data_store/polyphen/polyphen-2.2.2/bin/run_pph.pl -s test1033.fa test1033.coord 
 #o_acc               	 o_pos	o_aa1	o_aa2	rsid      	acc       	   pos	aa1	aa2	nt1	nt2	        prediction	            based_on	    effect	    site	  region	    PHAT	dScore	Score1	Score2	MSAv	  Nobs	 Nstruct	 Nfilt	PDB_id	PDB_pos	PDB_ch	 ident	lengthNormASA	SecStr	MapReg	  dVol	 dProp	B-fact	 H-bonds	 AveNHet	 MinDHet	 AveNInt	 MinDInt	 AveNSit	 MinDSit	Transv	CodPos	CpG	 MinDJxn	     PfamHit	  IdPmax	  IdPSNP	  IdQmin
 ENSSSCG00000001099ENSSSCT00000001195	   368	    S	    A	          	ENSSSCG00000001099ENSSSCT00000001195	   368	  S	  A	   	   	            benign	           alignment	          	        	        	        	+0.721	-1.180	-1.901	   2	    68	        	      	             	      	      	      	       	      	      	      	      	      	        	        	        	        	        	        	        	      	      	   	        	            	  12.350	  12.350	   42.63
 ENSSSCG00000001099ENSSSCT00000001195	   453	    R	    H	          	ENSSSCG00000001099ENSSSCT00000001195	   453	  R	  H	   	   	            benign	           alignment	          	        	        	        	+0.351	-2.130	-2.481	   2	    67	        	      	             	      	      	      	       	      	      	      	      	      	        	        	        	        	        	        	        	      	      	   	        	            	  33.194	  33.194	   93.76
 ENSSSCG00000001099ENSSSCT00000001195	   431	    K	    T	          	ENSSSCG00000001099ENSSSCT00000001195	   431	  K	  T	   	   	 possibly damaging	           alignment	          	        	        	        	+1.705	-1.678	-3.383	   2	    68	        	      	             	      	      	      	       	      	      	      	      	      	        	        	        	        	        	        	        	      	      	   	        	            	   2.382	        	   68.80

What goes in:

 test1033.fa
 >ENSSSCG00000001099ENSSSCT00000001195
 MSSIEQTTEILLCLSPAEAANLKEGINFVRNKSTGKDYILFKNKSRLKACKNMCKHQGGL
 FIKDIEDLNGRSVKCTKHNWKLDVSSMKYINPPGSFCQDELVVEKDEENGVLLLELNPPN
 PWDSEPRSPEDLAFGEVQITYLTHACMDLKLGDKRMVFDPWLIGPAFARGWWLLHEPPSD
 WLERLSRADLIYISHMHSDHLSYPTLKKLAERRPDVPIYVGNTERPVFWNLNQSGVQLTN
 INVVPFGIWQQVDKNLRFMILMDGVHPEMDTCIIVEYKGHKILNTVDCTRPNGGRLPMKV
 ALMMSDFAGGASGFPMTFSGGKFTEEWKAQFIKTERKKLLNYKARLVKDLQPRIYCPFAG
 YFVESHPSDKYIKETNIKNDPNELNNLIKKNSEVVTWTPRPGATLDLGRMLKDPTDSKGI
 VEPPEGTKIYKDSWDFGPYLNILNAAIGDEIFRHSSWIKEYFTWAGFKDYNLVVRMIETD
 EDFSPLPGGYDYLVDFLDLSFPKERPSREHPYEEIRSRVDVIRHVVKNGLLWDDLYIGFQ
 TRLQRDPDIYHHLFWNHFQIKLPLTPPDWKSFLMCSG 

 test1033.coord
 ENSSSCG00000001099ENSSSCT00000001195 368        S A
 ENSSSCG00000001099ENSSSCT00000001195 453        R H
 ENSSSCG00000001099ENSSSCT00000001195 431        K T

Provean

 >ENSSSCP00000018263 pep:novel chromosome:Sscrofa10.2:12:6621092:6624938:1 gene:ENSSSCG00000017236 transcript:ENSSSCT00000018765 gene_biotype:protein_coding t 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

 ## PROVEAN scores ##
 # 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