Error while annotating with a hg19 based VCF file

[kokyriakidis]

Hello!

I am getting an error when I try to annotate a VCF file which is based on hg19.

You can find the vcf file and the log file in the given URL:

https://drive.google.com/drive/folders/1jjwGNmujaNm8Wx9iaoeUIlTk7UsGQTM6?usp=sharing

[kokyriakidis]

It somehow worked now bit still get an error.

log2.txt

Also what's wrong with my case control file? The file contains two columns, with whitespace as the delimiter as stated in the wiki page.

cohort.txt

Edit: I managed to get it work using the alternative notation

STIFF_ANALYSIS-gatk-haplotype-annotated.vcf__F case
STIFF_ANALYSIS-gatk-haplotype-annotated.vcf__Gm case
STIFF_ANALYSIS-gatk-haplotype-annotated.vcf__Ev case
STIFF_ANALYSIS-gatk-haplotype-annotated.vcf__B control

How many controls do you think we need to have in order to get credible results?

It would be nice if there was an option to input a VCF file of controls (eg from 1KGP) and to contrast agaist the variants in another VCF file with the cases. For example I have to analyse 11 case samples with a very rare disease. I analysed them using GATK variant calling pipeline. It would be nice if I could contrast this VCF with a precomputed VCF I have with the 1KGP samples.

[kmoad]

Sorry for the delayed response. We are currently working on better management of multiple vcf files as part of a general update to how OpenCRAVAT handles cohorts. Briefly, it will be possible to identify groups of samples based on their input file. We'll update more as that release progresses.