Question: when use vcf-merge and vcf-concat
gravatar for Anop Singh Ranawat
5.6 years ago by
Anop Singh Ranawat0 wrote:

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 

how to use vcftool perl script...

sequencing snp • 2.5k views
ADD COMMENTlink written 5.6 years ago by Anop Singh Ranawat0

what have you tried ?

ADD REPLYlink written 5.6 years ago by Pierre Lindenbaum130k

Please add information and examples to this question.

ADD REPLYlink written 5.6 years ago by Michael Dondrup47k

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.

ADD REPLYlink written 5.6 years ago by ivivek_ngs5.0k
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