Variant annotation tutorial: Difference between revisions
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gunzip -c Bos_taurus.UMD3.1.78.gtf.gz | awk '$3=="gene"' | awk '$1==18&&$4>1000000&&$4<2000000' | 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 == | == Variant Effect Predictor == | ||
Revision as of 13:08, 6 March 2015
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
something
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