How to merge different VCF files

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3.1 years ago

Elisa • 0

Hi everyone,

I have 2 different VCF files (v4.3) : one containing SNP and Indels and the other one containing CNVs. The latter has only the mandatory fields (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO) while the former has also the field FORMAT and one reference genotype.

How can I merge these 2 VCF files?

Thanks in advance.

VCF • 1.1k views

ADD COMMENT • link written 3.1 years ago by Elisa • 0

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SNP and Indels and the other one containing CNVs.

why would you need to merge those files? what's your aim ?

ADD REPLY • link 3.1 years ago by Pierre Lindenbaum 164k

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We would like to annotate the variants on QCI-I. Do you suggest us to launch two separate analysis (so one for the annotation of SNP and Indels VCF file and one for the annotation of CNV VCF file) ?

ADD REPLY • link 3.1 years ago by Elisa • 0

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A tool to annotate one VCF file with INFO records of another VCF taking SNP into account?

ADD REPLY • link 3.1 years ago by zx8754 12k

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