[Samtools-help] documentation regarding samtools phase

[Kathleen K. <kat...@gl...>]

Hello,

Can anyone point me to documentation regarding Samtools phase? For instance, there is an option -A to drop ambiguous reads but I can’t find a description for how reads are determined ambiguous. Also, a general idea of the underlying algorithm would be helpful, as well as a workflow. From my understanding, generally in phasing one finds variants first, then uses those to phase, but it appears with this tool you input just the bam file, and then call variants from that. Any help/pointers are much appreciated!

Thanks,
Kathleen 
kat...@gl... <mailto:kat...@gl...>