i have two folder snp and indel , both folder have vcf file chromosome wise 1...22 , i want to make one vcf file of all vcf file of both folder ....so
how to use vcftool perl script...
what have you tried ?
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You have to be specific what you want to see? Usually you can do away with merging or concat them. If your intention is to look at the genes that are common or in total then simply annotate them and then merge the genes. Or if you want to remove the SNPs near INDELs then you have to compare the vcf files with vcf-compare or just convert them to bed files and compare. The vcftool is quite heavily documented and should not be difficult to use for things you are asking for in simple terms.