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From: Mahya M. <ma...@gm...> - 2020-06-29 14:43:34
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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 |