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Merge SNP & INDEL vcf files

I am creating a gene sequence for a sample in the vcf using a standard reference genome. The command for generating the sequence I found on this site works well.

samtools faidx ref.fasta chrom:start-stop | bcftools consensus -s sample my.vcf

But I have separate SNP and INDEL vcf files generated using GATK UnifiedGenotyper. I would like to merge these files so I can generate a consensus sequence from a reference. I want to include the INDELS but I am having trouble finding information on what happens with common tools used to join these vcf files.

Tools like: GATK CombineVariants

Any ideas would be appreciated.

Thanks

snp vcf indel
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written by mplace • mplace

but I am having trouble finding information on what happens with common tools used to join these vcf files. Tools like: GATK CombineVariantsGATK CombineVariants

and what do you want to know ?

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written by Pierre Lindenbaum Pierre Lindenbaum

The PI I work for would like to be able to generate strain specific gene sequences which include both snps and indels for the generation of PCR primers etc...

What happens when I combine the snp and indel vcf and there are overlapping sites?

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written by mplace • mplace

Please use ADD REPLY to answer to earlier comments, as such this thread remains logically structured and easy to follow. I now moved your comment, but as you can see that's not optimal.

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written by WouterDeCoster WouterDeCoster

What happens when I combine the snp and indel vcf and there are overlapping sites?

1) try and see. 2) If the SNP and the INDEL share the same REF allele, i would say GATK produces only one variant. Else two variants will be created.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you for the help.

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written by mplace • mplace

furthermore, GATK combine variant has a parameter to prioritize the source of genotypes.

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written by Pierre Lindenbaum Pierre Lindenbaum

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