[ensembl-dev] FW: Loftee and VCFCols Difficulties via port 3337

[Will McLaren]

Hi Alex,

Regarding issue 1, have you considered using VCF output instead of the
default tab-delimited output?
http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#vcfout

Have you tried contacting the VAX authors? Michael Yourshaw is usually very
responsive when I have communicated with him in the past.

I'm sure you can appreciate we have to prioritise debugging and fixing our
own code, but please do get back to us if you still have any outstanding
issues.

You may also like to try another available LoF plugin, LOFTEE from Daniel
MacArthur's lab: https://github.com/konradjk/loftee

Regards

Will McLaren
Ensembl Variation

On 9 October 2015 at 03:22, Alex Beesley <Alex.Beesley at telethonkids.org.au>
wrote:

> Dear Team
>
> I am experiencing significant difficulties with both the LoF.pm and
> VCFCols.pm plugins with VEP (FYI I am using a GRCh37 cache downloaded using
> the installer script and default settings (ensembl-tools release-82)).
>
> # Issue 1
> I want to use VCFCols.pm in order to obtain the original REF and ALT
> alleles from the VCF (to aid with interpretation of complex variants).
> However it seems that the only way to run VCFCols.pm plugin is in the
> online mode – if one tries to run it in offline mode (see first code
> example below), VEP returns an error relating to
> "$config->{ga}->fetch_by_transcript_stable_id($transcript_id)”. However,
> when running online (see second code example), it is extremely slow. This
> is incredibly frustrating because I do not wish to use any of the VAX
> functionality or its related databases, I simply wish to grab the original
> REF, ALT and other VCF column headers (including the genotypes and FORMAT
> fields) in my VEP output. Is there another way to grab the original VCF
> columns in the VEP output other than using VCFCols.pm? Or a way to modify
> the plugin such that it can work offline?
>
> perl ${VEP}/variant_effect_predictor.pl -i ${INPUT_VCF} -o
> ${INPUT_VCF%*.vcf}.vep --cache --assembly GRCh37 --offline \
>
>         --force_overwrite --check_existing --fork 24 \
>
>         --everything --flag_pick \
>
>         --plugin CADD,${CADD_SNV},${CADD_INDEL} \
>
>         --plugin ExAC,${EXAC} \
>
> —-plugin VCFCols \
>
>         --plugin
> LoF,human_ancestor_fa:/home/san/alex/.vep/Plugins/loftee-master/human_ancestor.fa.gz
> \
>
>         --fields
> Uploaded_variation,Location,REF,ALT,INFO,FORMAT,LoF,LoF_filter,LoF_flags,CADD_RAW,CADD_PHRED,ExAC_AF
>
>
>
> perl ${VEP}/variant_effect_predictor.pl -i ${INPUT_VCF} -o
> ${INPUT_VCF%*.vcf}.ONLINE.vep --cache --assembly GRCh37 --port 3337 \
>
>         --force_overwrite --check_existing --fork 24 \
>
>         --everything --flag_pick \
>
>         --plugin CADD,${CADD_SNV},${CADD_INDEL} \
>
>         --plugin ExAC,${EXAC} \
>
> —-plugin VCFCols \
>
>         --plugin
> LoF,human_ancestor_fa:/home/san/alex/.vep/Plugins/loftee-master/human_ancestor.fa.gz
> \
>
>         --fields
> Uploaded_variation,Location,REF,ALT,INFO,FORMAT,LoF,LoF_filter,LoF_flags,CADD_RAW,CADD_PHRED,ExAC_AF
>
>
>
> # Issue 2
> When running VEP in either of the two modes shown above, I obtain
> different confidence calls from the LoF.pm in regards to frameshift
> mutations. Specifically, for the example shown below, the LoF.pm plugin
> will call the variant HC (high confidence) in ONLINE mode, but LC (low
> confidence) when running offline. The particular flag thrown up for the LC
> call relates to non-canonical intron splice sites, however I have checked
> this particular variant on UCSC and the splice appear to be canonical, thus
> the ONLINE vep output is correct, and the offline appears to be incorrect.
> Since I am using a local cache (and I have also tried using a local fasta
> file), I am at a loss to explain why I would get completely different
> results by these two approaches for a LoF call. As mentioned above, my
> cache was downloaded using the installer script and default settings
> (ensembl-tools release-82).
>
>
>
> # Running Offline
>
> #Uploaded_variation               Consequence        IMPACT  LoF
>
> 10_126691951_C/- - 10:126691951 - frameshift_variant  HIGH   LC
> NON_CAN_SPLICE_SURR
>
> 10_126692023_G/- - 10:126692023 - frameshift_variant  HIGH   LC
> NON_CAN_SPLICE_SURR
>
>
> # Running Online
>
> #Uploaded_variation               Consequence        IMPACT  LoF
>
> 10_126691951_C/- - 10:126691951 - frameshift_variant  HIGH   HC
>
> 10_126692023_G/- - 10:126692023 - frameshift_variant  HIGH   HC
>
>
>
> I appreciate that neither VCFCols.pm nor LoF.pm were developed by your
> team, but I would be very grateful if you could help me on these issues
> as I have been struggling to get VEP customised for my needs for some time
> now. In regards to issue 1, I believe a lot of your users would benefit
> from a tool that could grab the original VCF headers in the VEP output, and
> in regards to the second issue, there must be something strange going on in
> regards to compatibility with the downloaded caches and the online
> databases but I am at a loss to explain it.
>
>
> Many thanks in advance
>
> Alex  Beesley
>
> Telethon Kids Institute
> Perth, Western Australia
>
>
>
>
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