[ensembl-dev] VEP does not annotate all rows in a samtools VCF

[Marlies Dolezal]

hi all,

i am using the latest VEP version 75 (API)(75) to annotate samtools VCF
files.

-offline --force_overwrite --species bos_taurus --fork 16 --input_file
Chr$i.vcf --o Chr$i.vep


the General statistics section of the VEP_summary.html tells me that all
lines of my vcfs are read in, but only a subset of these are processed.
eg:
Lines of input read 900857
Variants processed 900241

the difference in lines does not correspond to header/comment lines only.

where can i find out which variants are not processed to try to figure out
why they are not processed?

thanks a lot in advance
regards Marlies






--
Dr. Marlies Dolezal
1030 Vienna
Austria/Europe

marlies.dolezal(at)gmail.com

“The great tragedy of science is the slaying of a beautiful hypothesis by
an ugly fact.”
Thomas Henry Huxley
(1825-1895)
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