getting haplotype and diplotype information from a batch of WGS data

Question

[J.F.Jiang]

Hi all,

Suppose I have 1000 WGS data, for example, the 1000G data,

how can I get the confident haplotype and diplotype information for each sample? Is there any well-done pipeline to do such a job?

Should I use phasing program to carry out such a job? And how, is there any recommended soft?

Thanks,
Junfeng

Answer 1

[Devon Ryan]

If you need haplotype information, then phasing will normally be useful. In general, any tool that can call variants can also phase them. Both samtools and GATK provide methods to phase calls (freebayes probably does as well).