[ensembl-dev] Bug with HGVS Representation while running VEP

Cyriac Kandoth kandoth at cbio.mskcc.org
Fri Jan 22 19:14:51 GMT 2016


Hey Priti,

I have had related problems with the FASTA index when using older versions
of Perl or older BioPerl (
http://lists.ensembl.org/pipermail/dev/2014-October/010492.html). Since we
were unable to update the system Perl on our cluster, the only solution was
to compile Perl from source, to set it up as a local installation along
with all it's libraries. Below are the commands I followed to do this. Let
us know if this fixes the issue, or not.

~Cyriac

--

# To make the commands below easier, set a temporary env variable to point
to your current folder where you want to set up a local install of Perl:
export PERL_BASE="/opt/common/CentOS_6-dev/perl/"
cd $PERL_BASE

# Download Perl source tarball into a subfolder src:
wget -P src http://www.cpan.org/src/5.0/perl-5.22.0.tar.gz

# Untar into properly versioned subfolder:
tar -zxf src/perl-5.22.0.tar.gz

# Configure and build (can take a while):
cd perl-5.22.0
./Configure -des -Dprefix=$PERL_BASE/perl-5.22.0
-Dotherlibdirs=$PERL_BASE/perl-5.22.0/lib/perl5
make
make install
cd ..

# Install dependencies of OncoKB, VEP, and other tools we use:
curl -L http://cpanmin.us | $PERL_BASE/perl-5.22.0/bin/perl - --notest
-l $PERL_BASE/perl-5.22.0 JSON::Parse XML::Parser XML::Simple Encode LWP
LWP::Simple LWP::Protocol::https Archive::Extract Archive::Tar Archive::Zip
CGI DBI Time::HiRes

# Test running VEP using this new Perl:
$PERL_BASE/perl-5.22.0/bin/perl variant_effect_predictor.pl ...

On Fri, Jan 22, 2016 at 7:51 AM, Sarah Hunt <seh at ebi.ac.uk> wrote:

>
> Hi Priti,
>
> We have seen this issue when there are problems with the fasta file or
> it's index. If you are happy the fasta file is fine, deleting the index
> file and letting VEP re-build it usually resolves the poblem. Also, do
> check you are using BioPerl version 1.6.1 or later as we have seen problems
> with earlier versions.
>
> Best wishes,
>
> Sarah
>
>
> On 21/01/2016 16:15, Priti Kumari wrote:
>
>
> Hello,
>
> I ran two instances of VEPv83 on a large file with 50000 variants. I am
> getting different output, when I compare two output files. One, example is
> different c. value.
> v1 :
> PTEN  0       .       GRCh37  10      89692904        89692904
> +       Nonsense_Mutation       SNP     C       C       T
> rs121909224             TUMOR   NORMAL  C       C       c.388G>T
> p.Arg130Ter     p.R130* ENST00000371953
>
> v2:
> PTEN  0       .       GRCh37  10      89692904        89692904
> +       Nonsense_Mutation       SNP     C       C       T
> rs121909224             TUMOR   NORMAL  C       C         c.388C>T
> p.Arg130Ter     p.R130* ENST00000371953
>
> Command used for running both instances :
>
> /usr/bin/perl variant_effect_predictor//variant_effect_predictor.pl
> --species homo_sapiens --assembly GRCh37 --offline --no_progress --no_stats
> --sift b --ccds --uniprot --hgvs --symbol --numbers --domains
> --gene_phenotype --regulatory --canonical --protein --biotype --uniprot
> --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing
> --check_alleles --check_ref --total_length --allele_number --no_escape
> --xref_refseq --failed 1 --vcf --minimal --flag_pick_allele --pick_order
> canonical,tsl,biotype,rank,ccds,length --dir .vep/ --fasta
> .vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
> --input_file OP_VARIANT.vcf --output_file OP_VARIANT.v1.vep.vcf  --polyphen
> b --gmaf --maf_1kg --maf_esp --plugin
> ExAC,/.vep//ExAC.r0.3.sites.minus_somatic.vcf.gz --fork 4
>
> Any idea why this is happening?
> Thank you,
>
> --
> Priti Kumari
> Bioinformatics Engineer
> Department of Biostatistics and Computational Biology
> Dana-Farber Cancer Institute
> 3 Blackfan Cir,
> Center for Life Science Boston, Room 11037,
> Boston, MA 02115617-632-6133
>
>
>
>
>
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