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.
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hrenchert747 •
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.
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.
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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?