phasing VCF

Question

[bouchenak.chuxi]

Hello,

interested in haplotypes information, I'm looking for the best available tool i can use to automatically phase unphased VCF file. It was generated after aligning short reads sequencing of many crops samples to the reference.

I tied to look for some tools i found whatshap and the python package PPP . the last one didn't work well (gives an empty output)

have anyone used them in this purpos ? or has better suggestions?

Thank you !

[iraun]

I always use the tool you mentioned, whatshap, for phasing VCFs. Another popular tool that I know of is phASER.

[bouchenak.chuxi]

i'll give that a try , thank you iraun !