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Dbnsfp33 running time #243
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In the LOG (the "NOTICE" message printed on screen, what does it say?
Also, try to use table_annovar and dbnsfp42a
…On Wed, Apr 24, 2024 at 6:40 AM tahirasma ***@***.***> wrote:
Greetings,
I am trying to run the VCF file of 38,000 variants. The rest of the
databases run effiicently but it's taking almost 20-30 minutes in dbnsfp
(although the index is generated) annotation. Please advice if there is a
way to make it faster. The command is as follows:
annotate_variation.pl -filter -dbtype dbnsfp33 -buildver hg38 -outfile
./output_dbnsfp
Regards,
Asma Tahir
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The output was as follows: `NOTICE: Processing operation=f protocol=dbnsfp33 NOTICE: Running system command <annotate_variation.pl -filter -dbtype dbnsfp33 -buildver hg38 -outfile .input_file.filtered_filtered_dbnsfp .input_file.filtered_filtered_dbnsfp.avinput ./dbs/ -otherinfo> |
There is no error in the message below, so I think it is just the way how
your VCF file is generated. Basically >20% of the genome bins are scanned,
so indexing provides limited help to speed up.
Also, dbnsfp47a and dbnsfp47c are updated now on hg19/hg38 coordinate.
…On Thu, Apr 25, 2024 at 2:40 AM tahirasma ***@***.***> wrote:
The output was as follows:
NOTICE: Processing operation=f protocol=dbnsfp33
NOTICE: Finished reading 66 column headers for '-dbtype dbnsfp33'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype
dbnsfp33 -buildver hg38 -outfile .input_file.filtered_filtered_dbnsfp
.input_file.filtered_filtered_dbnsfp.avinput ./dbs/ -otherinfo>
NOTICE: Output file with variants matching filtering criteria is written
to .input_file.filtered_filtered_dbnsfp.hg38_dbnsfp33_dropped, and output
file with other variants is written to
.input_file.filtered_filtered_dbnsfp.hg38_dbnsfp33_filtered
NOTICE: Processing next batch with 38289 unique variants in 38289 input
lines
NOTICE: Database index loaded. Total number of bins is 101730 and the
number of bins to be scanned is 21655
NOTICE: Scanning filter database ./dbs/hg38_dbnsfp33.txt...Done
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Greetings,
I am trying to run the VCF file of 38,000 variants. The rest of the databases run effiicently but it's taking almost 20-30 minutes in dbnsfp (although the index is generated) annotation. Please advice if there is a way to make it faster. The command is as follows:
annotate_variation.pl -filter -dbtype dbnsfp33 -buildver hg38 -outfile ./output_dbnsfp
Regards,
Asma Tahir
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