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Phased genotype in the VCF #9

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bsb2014 opened this issue Aug 22, 2023 · 1 comment
Closed

Phased genotype in the VCF #9

bsb2014 opened this issue Aug 22, 2023 · 1 comment

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@bsb2014
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bsb2014 commented Aug 22, 2023

Hi there

I assembled several human genomes, mapped their short reads to their de novo assemblies, called snps, and phased them using long reads. Because the references are different, I would like to convert vcf to the same reference gh38. Is it possible to use the transanno for that?

I saw the transanno can swap ref/alt. I am wondering if it also swaps the phased genotypes? such as 0|1 to 1|0 due to the ref swap.

Thanks
@bsb2014
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bsb2014 commented Aug 24, 2023

I think transanno will do.

"rewrite allele frequency, INFO tags, FORMAT tags and a GT tag if REF and ALT columns are swapped."

@bsb2014 bsb2014 closed this as completed Aug 24, 2023
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