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konradjk / loftee

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GRCh38 branch does not work with GRCh37 data #109

Open yunkaig opened 3 months ago

yunkaig commented 3 months ago

Hi @konradjk,

I have both GRCh38 and GRCh37 data to run loftee. With the GRCh38 branch, my GRCh38 runs OK but GRCh37 cannot run.

I made sure I used the GRCh37 version of human_ancestor fa file, the conservation_file and the gerp_bigwig downloaded from http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/All_hg19_RS.bw.

It threw this error:

DBD::SQLite::db prepare failed: no such table: phylocsf_summary at /g/data/jb96/software/vep/vep_cache/Plugins_GRCh38/LoF.pm line 556, <__ANONIO__> line 2459.
WARNING: Plugin 'LoF' went wrong: Can't call method "execute" on an undefined value at /g/data/jb96/software/vep/vep_cache/Plugins_GRCh38/LoF.pm line 557, <__ANONIO__> line 2459.

So I tried to look into the conservation sql files and I found they have different tables in GRCh37 & 38.

sqlite> .open conservation_file_grch37.sql
sqlite> .tables
gerp_exons     phylocsf_data
sqlite> .open conservation_file_grch38.sql
sqlite> .tables
phylocsf_summary

I don't think that difference is expected. Could you fix the sql file and upload if possible? Or is there a way for me to fix that locally?

Many thanks, Yunkai