LoFTool in table_annovar.pl about doc-annovar

[kaichop]

operation is f

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On Thu, Mar 30, 2017 at 3:41 PM, Robert Butler ***@***.***> wrote: I am not sure I have the correctly formatted loftool database. I downloaded the file from the readthedocs website (LoFtool_scores.txt) and renamed it to /opt/annovar/humandb/hg19_loftool.txt but when I run table_annovar.pl with this command: table_annovar.pl rslist.avinput ${annovar}humandb/ -buildver hg19 -out rslist -remove -protocol dbnsfp33a,exac03,gnomad_exome,clinvar_20170130,loftool -operation f,f,f,f,g -nastring "-" I get correct outputs for every other operation but loftool: NOTICE: Processing operation=g protocol=loftool NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype loftool -outfile rslist.loftool -exonsort rslist.avinput /opt/annovar/humandb/> NOTICE: Output files were written to rslist.loftool.variant_function, rslist.loftool.exonic_variant_function NOTICE: Reading gene annotation from /opt/annovar/humandb/hg19_loftool.txt ... Error: invalid record in /opt/annovar/humandb/hg19_loftool.txt (>=11 fields expected in loftool gene definition file): Error running system command: <annotate_variation.pl -geneanno -buildver hg19 -dbtype loftool -outfile rslist.loftool -exonsort rslist.avinput /opt/annovar/humandb/> Do I need to process the Loftool file prior to running annovar (it only has two columns, << 11 it is looking for)? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuGAXmwaftCj2Pn1k4BuOj8TokhYoks5rrAVWgaJpZM4Mu1B5> .

[rbutleriii]

Running the operation as f I get this message:

NOTICE: Scanning filter database /opt/annovar/humandb/hg19_loftool.txt...Error: invalid database entry (generic ANNOVAR database should contain at least 4 tab-delimited fields per line):
Error running system command: <annotate_variation.pl -filter -dbtype loftool -buildver hg19 -outfile rslist rslist.avinput /opt/annovar/humandb/>

Head of file from http://www.openbioinformatics.org/annovar/download/LoFtool_scores.txt.gz :
Gene LoFtool_percentile
NIPBL 6.89E-05
SCN1A 1.38E-04
NOTCH1 2.07E-04
TSC2 2.76E-04
PTCH1 3.44E-04
SCN5A 4.13E-04
EP300 4.82E-04
CACNA1C 5.51E-04

[kaichop]

Okay I see. loftool is a gene score, similar to pLI or RVIS. It cannot be used in the current version of ANNOVAR. It is provided for users to post-filter their results and identify causal genes.

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On Thu, Mar 30, 2017 at 4:21 PM, Robert Butler ***@***.***> wrote: Running the operation as f I get this message: NOTICE: Scanning filter database /opt/annovar/humandb/hg19_loftool.txt...Error: invalid database entry (generic ANNOVAR database should contain at least 4 tab-delimited fields per line): Error running system command: <annotate_variation.pl -filter -dbtype loftool -buildver hg19 -outfile rslist rslist.avinput /opt/annovar/humandb/> Head of file from http://www.openbioinformatics. org/annovar/download/LoFtool_scores.txt.gz : Gene LoFtool_percentile NIPBL 6.89E-05 SCN1A 1.38E-04 NOTCH1 2.07E-04 TSC2 2.76E-04 PTCH1 3.44E-04 SCN5A 4.13E-04 EP300 4.82E-04 CACNA1C 5.51E-04 — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuJEilKsxQeUCfYzR0o7lXklP72Qxks5rrA7dgaJpZM4Mu1B5> .