Merge hg38 branch to master?

[Hoeze]

Dear @konradjk, would it be possible to merge the hg38 with current master s.t. we have one LOFTEE version that works for both hg19 and hg38?

It's currently very hard to install and use LOFTEE for hg38. For example, I'm constantly failing to get the hg38 branch working because of conflicting LoF.pm from VEP. Also, I had a very hard time to figure out which files are needed and which options need to be set since e.g. gerp_bigwig does not exist on master.

I believe that a merged version of LOFTEE would significantly simplify its usage.

[Stikus]

Any news about merge? In this issue mentioned some differences between branches: https://github.com/konradjk/loftee/issues/56

I've simple installed different assemblies in different folders, but this is not very elegant solution and I have to use different directory than for all other VEP plugins.

[Hoeze]

@konradjk What about merging this branch from @willmclaren? https://github.com/willmclaren/loftee

[Hoeze]

Another hint for the record: If you use ensembl-vep from bioconda, you NEED to delete the plugin from the share folder:

VEP_SHARE=$CONDA_PREFIX/share/ensembl-vep-$VERSION

rm $VEP_SHARE/TissueExpression.pm \
  $VEP_SHARE/ancestral.pm \
  $VEP_SHARE/context.pm \
  $VEP_SHARE/de_novo_donor.pl \
  $VEP_SHARE/extended_splice.pl \
  $VEP_SHARE/gerp_dist.pl \
  $VEP_SHARE/loftee_splice_utils.pl \
  $VEP_SHARE/splice_site_scan.pl \
  $VEP_SHARE/svm.pl \
  $VEP_SHARE/utr_splice.pl

Afterwards, you can set PERL5LIB to the correct LOFTEE source folder.

[mhebrard]

Hi here ! I am using the docker image created by willmclaren but still no LoF annotation in my VEP output... any chance or hint what is missing ?

/vep -i /opt/vep/.vep/input.txt --json --cache --merged --no_stats --species homo_sapiens --assembly GRCh38 --plugin LoF,loftee_path=/opt/vep/src/ensembl-vep/loftee,data_path=/opt/vep/.vep/loftee_data -o STDOUT

• input.txt contain a small list of variant I expect loftee to flag (extracted from gnomad)
• loftee path is in the PREL5LIB and LoF.pm is inside this directory
• I downloaded gerp_conservation_scores.homo_sapiens.GRCh38.bw, human_ancestor.fa.gz, phylocsf_gerp.sql for GRCh38 into the data_path directory

[willmclaren]

@mhebrard I wouldn't use the docker image you refer to - it is >3 years old and to be honest I can't remember why/how it was created!

You might get some debug info by adding --safe to your command line.

If someone wants to have a go creating an up-to-date docker image then be my guest.

[mhebrard]

@willmclaren, thanks for the hint on --safe that allowed me to understand what was wrong. I got the error:

Failed to compile plugin LoF: Can't locate [LoF.pm](http://lof.pm/) in @INC (you may need to install the LoF module) (@INC contains: /opt/vep/.vep/Plugins /opt/vep/src/ensembl-vep/modules /opt/vep/src/ensembl-vep /opt/vep/src/bioperl-live /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at (eval 51) line 2.

I tried to specify the correct path to LoF.pm using $PERL5LIB and loftee_path without success...

Then I copy the content of loftee folder into .vep/Plugins and that worked ! With in addition the few data files mentioned in the README to download into /vep/Plugins/data:

• gerp_conservation_scores.homo_sapiens.bw
• human_ancestor.fa.gz
• human_ancestor.fa.gz.fai
• human_ancestor.fa.gz.gzi
• phylocsf_gerp.sql

Note that the link to gerp_conservation_scores.homo_sapiens.bw did not work. I had to use this instead and rename to file to fit the requirements

Hope that help others