dbNSFP plugin only producing empty columns

[Hepit]

dbNSFP plugin only producing empty columns

[nakib103]

Hello @Hepit,

Thanks for your query!

I tried with dbNSFP v4.4a and could not reproduce the issue for the variant example you have provided. One thing to make sure is that you have correctly processed the dbNSFP file. To see, how to process the file you can check the DESCRIPTION section of the plugin.

Once that done, can you make sure you can correctly do tabix on the dbNSFP file. For example, the following query should work -

$ tabix ${db}/dbNSFP4.4a/dbNSFP4.4a_grch38.gz 10:180064-180064 | awk '$4 == "G"'
10	180064	C	G	L	V	.	10	226004	10	216004	18;18;18;18;18;18;18;18;18;18;18;18	ZMYND11;ZMYND11;ZMYND11;ZMYND11;ZMYND11;ZMYND11;ZMYND11;ZMYND11;ZMYND11;ZMYND11;ZMYND11;ZMYND11	ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171;ENSG00000015171	ENST00000439456;ENST00000397962;ENST00000397959;ENST00000309776;ENST00000509513;ENST00000381591;ENST00000403354;ENST00000381607;ENST00000402736;ENST00000602682;ENST00000397955;ENST00000558098	ENSP00000397072;ENSP00000381053;ENSP00000381050;ENSP00000309992;ENSP00000424205;ENSP00000371003;ENSP00000385484;ENSP00000371020;ENSP00000386010;ENSP00000473321;ENSP00000381046;ENSP00000452959	E9PE09;Q15326;Q15326-5;B7Z2J6;Q15326-6;Q15326;B0QZE2;Q15326-2;E7ENI9;Q15326-5;E7EV75;Q15326-3	E9PE09_HUMAN;ZMY11_HUMAN;ZMY11_HUMAN;B7Z2J6_HUMAN;ZMY11_HUMAN;ZMY11_HUMAN;B0QZE2_HUMAN;ZMY11_HUMAN;E7ENI9_HUMAN;ZMY11_HUMAN;E7EV75_HUMAN;ZMY11_HUMAN	.;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;.;c.52C>G	.;p.L18V;p.L18V;p.L18V;p.L18V;p.L18V;p.L18V;p.L18V;p.L18V;p.L18V;.;p.L18V	c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G	p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val	c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G;c.52C>G	p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val;p.Leu18Val .....

Best regards,
Nakib

[Hepit]

@nakib103 thanks for your quick response !

I've processed it as was indicated, with the exception that no file was found to download at ftp://dbnsfp:[email protected]/dbNSFP4.4a.zip, so I got it from Amazon instead. The exact code I ran is :

version=4.4a
wget https://dbnsfp.s3.amazonaws.com/dbNSFP4.4a.zip
unzip dbNSFP${version}.zip
zcat dbNSFP${version}_variant.chr1.gz | head -n1 > h
zgrep -h -v ^#chr dbNSFP${version}_variant.chr* | sort -k1,1 -k2,2n - | cat h - | bgzip -c > dbNSFP${version}_grch38.gz
tabix -s 1 -b 2 -e 2 dbNSFP${version}_grch38.gz

When running your query, no output is produced. It also looks like "dbNSFP4.4a_grch38.gz" only contains a header - in fact, when unzipped it is identical to file "h". Is it possible there is a typo in the zgrep command?

Thanks !
Elby

[nakib103]

Hi @Hepit,

The commands does not seems to have any problem. Can you make sure you have downloaded the dbNSFP files properly and they are not empty themselves. I would recommend downloading and processing the dbNSFP file from fresh and then try again.

Best regards,
Nakib

[Hepit]

I ended up running the various commands separately instead of with pipes, and that seems to have done the trick. Oddly enough, when running the series of pipes together (zgrep -h -v ^#chr dbNSFP${version}_variant.chr* | sort -k1,1 -k2,2n - | cat h - | bgzip -c > dbNSFP${version}_grch38.gz), the end file only contains a header. Not sure which one of them fails.

Thanks a lot for your help with this !