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Faster filtering of vcfs using split-vep over filter_vep

Dear Biostars,

I am trying to filter a multi-sample vcf which has been annotated with VEP in order to get a set of rare likely deleterious calls. However, the file is very large and using "filter_vep" is taking a very long time per file (>5 days per chromosome on a HPC environment). I have been told that the bcftools add-on:split-vep performs better for this and I was wondering how queries using this would look as I have been struggling.

For example:

filter_vep -i my.vcf -o my_filtered.vep --filter "(MAX_AF is  < 0.01 or not MAX_AF) and (CADD_PHRED gte 20 or not CADD_PHRED )"

Could one reproduce this using split-vep - I would want to output the entire vcf line (ideally with the header) so that it remains a vcf file?

Many thanks!

vep bcftools split-vep vcf
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written by tacrolimus tacrolimus

Hey omid.alavijeh ,

could you please show the header of the vcf file and the first few variants?

fin swimmer

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written by finswimmer finswimmer

Hi @finswimmer,

I work in an airlock environment so can't bring data out but it looks like this (taken from another site but basically the same).

head my.vcf
##fileformat=VCFv4.0
##VEP="v91" time="2018-01-04 23:07:28" cache="/home/davetang/.vep/homo_sapiens/91_GRCh37" ensembl-variation=91.c78d8b4 ensembl-io=91.923d668 ensembl=91.18ee742 ensembl-funcgen=91.4681d69 1000genomes="phase3" COSMIC="81" ClinVar="201706" ESP="20141103" HGMD-PUBLIC="20164" assembly="GRCh37.p13" dbSNP="150" gencode="GENCODE 19" genebuild="2011-04" gnomAD="170228" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO 
21      26960070        rs116645811     G       A       .       .       CSQ=A|missense_variant|MODERATE|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|10/11||||1043|1001|334|T/M|aCg/aTg|||-1||HGNC|14027,A|intron_variant|MODIFIER|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding||9/9||||||||||-1||HGNC|14027,A|upstream_gene_variant|MODIFIER|LINC00515|ENSG00000260583|Transcript|ENST00000567517|antisense|||||||||||4432|-1||HGNC|16019
21      26965148        rs1135638       G       A       .       .      CSQ=A|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|8/11||||939|897|299|G|ggC/ggT|||-1||HGNC|14027,A|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|8/10||||939|897|299|G|ggC/ggT|||-1||HGNC|14027,A|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000419219|protein_coding|8/8||||876|867|289|G|ggC/ggT|||-1|cds_end_NF|HGNC|14027
21      26965172        rs10576 T       C       .       .       CSQ=C|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|8/11||||915|873|291|P|ccA/ccG|||-1||HGNC|14027,C|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|8/10||||915|873|291|P|ccA/ccG|||-1||HGNC|14027,C|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000419219|protein_coding|8/8||||852|843|281|P|ccA/ccG|||-1|cds_end_NF|HGNC|14027
21      26965205        rs1057885       T       C       .       .      CSQ=C|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|8/11||||882|840|280|V|gtA/gtG|||-1||HGNC|14027,C|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|8/10||||882|840|280|V|gtA/gtG|||-1||HGNC|14027,C|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000419219|protein_coding|8/8||||819|810|270|V|gtA/gtG|||-1|cds_end_NF|HGNC|14027
21      26976144        rs116331755     A       G       .       .      CSQ=G|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|3/11||||426|384|128|L|ctT/ctC|||-1||HGNC|14027,G|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|3/10||||426|384|128|L|ctT/ctC|||-1||HGNC|14027,G|synonymous_variant|LOW|MRPL39|ENSG00000154719|Transcript|ENST00000419219|protein_coding|3/8||||393|384|128|L|ctT/ctC|||-1|cds_end_NF|HGNC|14027
21      26976222        rs7278168       C       T       .       .      CSQ=T|synonymous_variant|LOW|MRPL39|
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updated by finswimmer finswimmer • written by tacrolimus tacrolimus

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