[Vcftools-help] vcf-contrast

[Mahya M. <ma...@gm...>]

Mahya Mehrmohamadi <ma...@gm...>
5:34 PM (3 hours ago)
to anthony.marcketta
Hi

I'm having trouble finding a detailed description of what vcf-contrast
actually does. I have two groups of 10 samples that I'm trying to compare.
I ran vcf-contrast but i don't understand how the novelty score is
calculated and how to interpret it (e.g. what is considered a high
confidence score etc...). Here is the command I used:

vcf-contrast -n
+S790Nr526,S790Nr527,S790Nr528,S790Nr529,S790Nr530,S790Nr540,S790Nr541,S790Nr542,S790Nr543,S790Nr555
-S1189Nr1,S1189Nr3,S1189Nr6,S1246Nr21,S790Nr531,S790Nr532,S790Nr544,S790Nr545,S790Nr533,S790Nr539
/Users/mahya/Desktop/ImmunoDef/joint-genotyping/final-results/All.hg38.twist-exome-plus.joint-genotyping.vcf.gz
> /Users/mahya/Desktop/ImmunoDef/vcfContrast


I've also used other tools for this comparison such as SNPSift and the
results don't seem to have much overlap with the high scoring variants from
vcf-contrast.

Help would be much appreciated.
Best,
Mahya