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wdecoster / phasius

MIT License
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Visualize phase block with VCF file #2

Open Mon3trK opened 1 month ago

Mon3trK commented 1 month ago

Hi developer of phasius Is it possible to use VCF files as input for phasius since most phasing software produces phased .vcf file. Also, tt is relatively time consuming to run whatshap halpotag to rephase to bam file with phased vcf.

wdecoster commented 1 month ago

Hi,

That is currently not supported but is possible in principle. One difference will be that, when using BAM files, the beginning and end of a block will be the first and last nucleotide of a read, while for a VCF file, the beginning and end of a block will be the position of the first and last phased variant, and thus, those phase blocks shown from VCF will be (a bit) shorter.

That said, I don't know when I will be able to implement this, but I will do my best :-)

Wouter

Mon3trK commented 1 month ago

Hi @wdecoster thanks for the quick response. Maybe I can refer to someone who is familiar with rust to implement this and create a PR.

wdecoster commented 1 week ago

Hi,

I have added support for VCF files in v0.2.0 :) Making a new release now... Feedback always appreciated!

Best, Wouter

Mon3trK commented 1 week ago

Wow, that is great, i will try it recently.