Is there any GUI tool which can compare 200 VCFs and show different SNPs between all the samples?

Question

[hrenchert747]

Is there any GUI tool which can compare 200 VCFs and show different SNPs between all the samples? Have tried GATK, BCF tools, VarChest, VCFTools, NextGene project comparison, DNAStar, R packages. Is there a better solution available? Thank you.

[Jorge Amigo]

if you've tried all those programs I don't understand why you're after a GUI. maybe a simple combination of bash commands, such as cut -f1-5 *.vcf | grep -v ^# | sort -k1,1 -k2,2n | uniq -c | awk '{if($1==1)print $2}', would do?

Answer 1

[Frédéric Bigey]

Using GATK (not a GUI tool) CombineVariants you can read many VCF and combines them into a single VCFs. CombineVariants always produces a union of the input VCFs. Then any part of the Venn of the merged VCFs can be extracted using JEXL expressions on the set attribute using SelectVariants.

[hrenchert747]

GATK throws errors on VCF file comparison (VCFs from the NextGene software output). Please advise a better solution for the comparison of 50-300 VCF with an aim to find distinctive genes. Thanks.