WARNING: chromosome not in offsets

[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

[evatosco]

Thank you so much @sandeepyuva1994 for opening this issue, because I have the exact same problem by using the -v field from the test command:

../VVP \
-i ./mock001_raw_VEP_to_VAAST.vcf.gz \
-d gnomad.062717.build \
-v CSQ,4,6,1,15 \
1> ./mock001_raw_VAAST.vvp.out

I have compared the test vcf file from the GitHub repository to the vcf I generated by following all the steps for input (first vt, then vep, then bgzip and then used it as input for vaast). They are pretty different. I do not know if things have upgraded and changed since the test vcf file was generated, but something has to have changed.

I also have not been able to figure out what the CSQ parameter meant and if I have to change it or what I have to keep in mind to change it correctly.

Thanks!