how to use background based on gnomAD ?

[hsxsin]

hi
I I've successfully run the VVP,but I do know how to use background based on gnomAD? I download gnomad.062717.build.tar.gz and unzip it ，can not find gnomad.062717.build.bin and gnomad.062717.build.max.
can you provide some tips or command to build gnomAD background?

[stevendflygare]

I'm sorry to hear you are having problems getting the gnomAD background. If this is helpful, here is the md5sum of gnomad.062717.build.tar.gz: 410658dafc0ed3f65b3b51f04354a34a. Then if you:

tar -zxvf gnomad.062717.build.tar.gz

you should see 3 files:

gnomad.062717.build.bin
gnomad.062717.build.chr_offsets.txt
gnomad.062717.build.dist

These files are what you need to run VVP against the gnomad background.

[hsxsin]

when I run VVP:
VVP -i test.vep.vcf -d /VVPdatabase/gnomad.062717.build.bin -v CSQ,4,6,1,15 1
an error occurred:
FATAL: could not create mmap from /VVPdatabase/gnomad.062717.build.bin.dist

should I create background first? but build_background help Information said I should input VCF file。what should I do
Best wishes

[stevendflygare]

With the -d option, you want to give the prefix to the database. So it should look like -d /VVPdatabase/gnomad.062717.build

[hsxsin]

I use -d option,VVP -i test.vep.vcf -d /VVPdatabase/gnomad.062717.build -v CSQ,4,6,1,15 1
and can't execute:
FATAL: could not create mmap from /VVPdatabase/gnomad.062717.build.dist

[barrymoore]

Make sure that your background files definitely exist AND that they are writable. VVP doesn’t actually write to them but they do need to be set as writable Barry On May 1, 2018, at 7:30 PM, hsxsin <[email protected]<mailto:[email protected]>> wrote: I use -d option,VVP -i test.vep.vcf -d /VVPdatabase/gnomad.062717.build -v CSQ,4,6,1,15 1 and can't execute: FATAL: could not create mmap from /VVPdatabase/gnomad.062717.build.dist — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#6 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ACI421qtYVINNGfS8I4zwwvSEEyzqrDvks5tuQwugaJpZM4TfJnY>.

[jina-ali]

Hi,
when I run vvp:
VVP -i test_VEP.vcf -d gnomad.062717.build -v CSQ,4,6,1,15 1> test_VVP.out

I could have the raw scores (hemi_score,het_score, hom_score), but all the vvp scores (hemi_vvp,..) are equal to -1. what should I do?

[sandeepyuva1994]

Hi Steven,
I tried running vvp on a test sample data and but it gives 'WARNING: chromosome chrY not in offsets' error all chr, also I have not been able to figure what the CSQ parameter is about. If you clarify these, it would be helpful for my analysis.

command : ./VVP -i /test_sample.vcf -d /VVP-pub-master/gnomad.062717.build -v CSQ,4,6,1,15 1>test_sample.out
error : WARNING: chromosome chrY not in offsets