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gVCF to VCF conversion - 1000 Genomes Project data

Hello Biostars,

I want to use 1000 Genomes Project phase3 data. Is it possible to get gVCFs instead of VCFs ? If not, is there any way we can convert VCF to gVCFs??

Thank you in advance :)

sequencing snp next-gen
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updated by WouterDeCoster WouterDeCoster • written by anu014 anu014

This thread asks about gVCFs -> VCFs, maybe there's some info there.

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written by jonasmst jonasmst

1 answer

No, you cannot convert VCFs to gVCFs. Those files don't contain the required information for conversion. For getting the gvcf files you would have to repeat variant calling, starting from the bam file.

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written by WouterDeCoster WouterDeCoster

Can you elaborate what is that extra information required?

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written by anu014 anu014

Thank you for the help, I'll go through it :)

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written by anu014 anu014

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