Loftee is not annotating the file

[SarahRQazi]

Hi,

I am running loftee but while vep is annotating the file loftee does not. Here is my command

/home/hpcc/tools/ensembl-vep/./vep --cache --offline -i Input.vcf   --everything --force_overwrite -o Output.vcf --dir_plugins /home/hpcc/.vep/Plugins/loftee/
`

Is there something wrong with my command? Here are some lines header of output file.

## ENSEMBL VARIANT EFFECT PREDICTOR v93.3
## Output produced at 2018-09-26 00:33:37
## Using cache in /home/hpcc/.vep/homo_sapiens/93_GRCh38
## Using API version 93, DB version ?
## ensembl-io version 93
## ensembl-funcgen version 93
## ensembl version 93
## ensembl-variation version 93
## sift version sift5.2.2
## ESP version V2-SSA137
## genebuild version 2014-07
## COSMIC version 85
## regbuild version 16
## dbSNP version 150
## assembly version GRCh38.p12
## 1000genomes version phase3
## gnomAD version 170228
## polyphen version 2.2.2
## ClinVar version 201805
## gencode version GENCODE 28
## HGMD-PUBLIC version 20174
## Column descriptions:
## Uploaded_variation : Identifier of uploaded variant
## Location : Location of variant in standard coordinate format (chr:start or chr:start-end)
## Allele : The variant allele used to calculate the consequence
## Gene : Stable ID of affected gene
## Feature : Stable ID of feature

[konradjk]

Were there any errors when the run first started?

[SarahRQazi]

First there was the error of Failed to compile plugin Lof: Can't locate Lof.pm in @INC (you may need to install the Lof module) I solved this by manually downloading loftee from github. Then there was error of Argument "22_KI270928v1_alt" isn't numeric in numeric comparison (<=>) at /home/hpcc/tools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm line 745, <__ANONIO__> line 3722. I changed this string 22_KI270928v1_alt by sed command.

[konradjk]

Were there any other errors? That second one is only a warning, so that should be fine. Usually something would say there was a problem with the LoF plugin.

I also haven't tested it too much on GRCh38 so that could be an additional problem, but that doesn't explain this particular issue.

[SarahRQazi]

No there was msg of connection with Ensemble MySQL database which I resolved by solving offline option. Is there problem because I did not used human_ancestor.fa?

[konradjk]

That could be an issue, but I would assume it would error out if it wasn't going to give you output. We plan to put out a formal GRCh38 version soon, but this is not available yet.

[SarahRQazi]

Is there a way as to how should I work loftee?

[konradjk]

Could you post all of the output from when you invoke the command to when it's finished? Also, I just looked at the header and nothing seems particularly wrong (you mentioned that's some of the lines - can you post all of the header lines?)

[SarahRQazi]

It does not give any sort of output when I invoke the command. Here is complete header.

## ENSEMBL VARIANT   EFFECT PREDICTOR v93.3 --
## Output produced at 2018-09-26 03:50:18
## Using cache in   /home/hpcc/.vep/homo_sapiens/93_GRCh38
## Using API version 93, DB version ?
## ensembl-funcgen version 93
## ensembl-io version 93
## ensembl-variation version 93
## ensembl version 93
## HGMD-PUBLIC version 20174
## dbSNP version 150
## gencode version GENCODE 28
## regbuild version 16
## COSMIC version 85
## gnomAD version 170228
## assembly version GRCh38.p12
## polyphen version 2.2.2
## 1000genomes version phase3
## ESP version V2-SSA137
## ClinVar version 201805
## genebuild version 2014-07
## sift version sift5.2.2
## Column descriptions:
## Uploaded_variation : Identifier of   uploaded variant
## Location : Location of variant in   standard coordinate format (chr:start or chr:start-end)
## Allele : The variant allele used to   calculate the consequence
## Gene : Stable ID of affected gene
## Feature : Stable ID of feature
## Feature_type : Type of feature -   Transcript, RegulatoryFeature or MotifFeature
## Consequence : Consequence type
## cDNA_position : Relative position of   base pair in cDNA sequence
## CDS_position : Relative position of   base pair in coding sequence
## Protein_position : Relative position   of amino acid in protein
## Amino_acids : Reference and variant   amino acids
## Codons : Reference and variant codon   sequence
## Existing_variation : Identifier(s) of   co-located known variants
## Extra column keys:
## IMPACT : Subjective impact   classification of consequence type
## DISTANCE : Shortest distance from   variant to transcript
## STRAND : Strand of the feature (1/-1)
## FLAGS : Transcript quality flags