Comments (1)
I always keep unphased sites, I can then decide when running MSMC to remove them using the —skipAmbiguous flag.
Best wishes,
Stephan
On 26 Feb 2016, at 21:25, hhu1 [email protected] wrote:
I am using MSMC over genomes sequenced by Complete Genomics. Based on the Schiffels & Durbin 2014 paper, unphased sites would introduce bias for population split analysis. However, when I looked into run_shapeit.sh tool, it seems that phasing was performed only on SNVs present in shapeit2 reference panel. Afterwards, both phased and unphased sites were merged into the same vcf file.
My question is, should I keep the unphased sites (those not present in the reference phasing panel) in my vcf file? If not, should I somehow fix the mask file to reflect the fact that only sites present in the reference panel are callable?
Thanks very much for your suggestions,
Hao Hu
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Reply to this email directly or view it on GitHub #18.
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