can you give me an example command with run VEP?

[yubau1112]

I want to use Local VEP when use charger

my command is:

(CharGer) [yubau@cmuh-i2 Demo]$ charger -f clinvar_20200210.vep.vcf -o clinvar_20200210.vep.charger.ltEx.tsv -l -t -E -x --exac-vcf ExAC.r1.sites.vep.vcf --mac-clinvar-tsv clinvar_alleles.multi.b37.tsv.gz --perl /home/yubau/perl --vep-script /home/yubau/VEP/ensembl-vep/vep --vep-config /home/yubau/VEP/ensembl-vep/t/Config.t --vep-cache /home/yubau/.vep --vep-version 99 --vep-output clinvar_20200210_output.charger.vep.vcf --grch 37 --ensembl-release 75 --reference-fasta /home/yubau/.vep/homo_sapiens/99_GRCh37 --fork 48

any wrong?

Can you give me an example command when use charger with run VEP?

thanks

[ccwang002]

We will drop the support to call VEP directly from CharGer in future. It's better if you do it in two steps: 1) run VEP to annotate the VCF, and 2) run CharGer with the VEP annnotated VCF. If the two-step approach doesn't work, let us know.

[yubau1112]

So, you mean:

Local VEP (works with .vcf input only; suppresses ReST too): --perl Path to Perl --vep-script Path to VEP --vep-config config-file for VEP --vep-cache Path to VEP cache directory --vep-version VEP version (default = 87) --vep-output VEP output file (default = charger.vep.vcf) --grch assembly GRCh verion (default = 37) --ensembl-release Ensembl release version (default = 75) --reference-fasta VEP reference fasta --fork Number of forked processes used in VEP (default = 0)

you not Suggest use ”Local VEP ” function in charger ?

you say " If the two-step approach doesn't work, let us know."

yes, it's work, but I got so many warring message I really want to close warring message when run charger, have any way to close? Please don't tell me ignore

Can you give me an example? how??????

thanks

[yubau1112]

somebody found 3 bug (https://www.jianshu.com/p/544caf92b24c) :

/home/yubau/anaconda2/envs/CharGer/lib/python2.7/site-packages/biomine/webapi/entrez/entrezapi.py

Line 332 and Line 333 entrezaip ---need to modify---> entrezapi

/home/yubau/anaconda2/envs/CharGer/lib/python2.7/site-packages/charger/charger.py varSet ---need to modify---> varsSet

/home/yubau/anaconda2/envs/CharGer/lib/python2.7/site-packages/biomine/webapi/ensembl/ensemblapi.py

LINE 381 add "if len(vals) < 6 : continue"

but I will get more Warning

thanks

[ccwang002]

I am sorry that you have to bear with the warnings for a while, until we finish an update on CharGer. The warning doesn't affect the results.