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Heng Li 2014-11-17 15:23:38 -05:00
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@ -158,7 +158,8 @@ depth, clustered variants or weak alignment. We believe most hs38-only calls are
problematic. In addition, if we compare two NA12878 replicates from HiSeq X10
with nearly identical library construction, the difference is ~140k, an order
of magnitude higher than the difference between hs38 and hs38d6. ALT contigs,
decoy and HLA genes in hs38d6 improve variant calling at little cost.
decoy and HLA genes in hs38d6 improve variant calling and enable the analyses of
ALT contigs and HLA typing at little cost.
## Problems and Future Development