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===Specific Aims=== Table of current specific aims, to be completed within short time frames. Specific aims should make progress towards the completion of aims (above). {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> |- style="font-size:12pt" align="center" valign="bottom" |align="center" width="500" | '''Specific Aim''' |align="center" width="65" | Date to Completion |align="center" width="65" | Date of Completion |align="center" width="250" | Notebook Link |- style="font-size:12pt" align="center" valign="bottom" | height="15" align="left" | Combine PGP1 data from Complete Genomics WGS to create more defendable/accurate VCF | align="center" | January 1, 2016 | align="center" | | align="center" | [[Daniel:Notebook/Haplotyping/MergeVCF|Merging Complete Genomics WGS data]] |- style="font-size:12pt" align="center" valign="bottom" | height="15" align="left" | Comparing data sets using consistent pairs method | align="center" | January 1, 2016 | align="center" | | align="center" | [[Daniel:Notebook/Haplotyping/ConsistentPairs|Consistent Pairs Method]] |- style="font-size:12pt" align="center" valign="bottom" | height="15" align="left" | Use BEAGLE to get inferences for PGP1 | align="center" | August 1, 2015 | align="center" | | align="center" | [[Daniel:Notebook/Haplotyping/BEAGLE|Using BEAGLE to infer population data]] |- style="font-size:12pt" align="center" valign="bottom" | height="15" align="left" | Assess variant calling using freebayes, create ROC | align="center" | January 1, 2016 | align="center" | | align="center" | [[Danie:Notebook/Haplotyping/Genotyping|Genotyping Samples]] |- style="font-size:12pt" align="center" valign="bottom" | height="15" align="left"| Combine Hi-C and BAC data to get more complete haplotypes | align="center" | August 1, 2015 | align="center" | | align="center" | [[Daniel:Notebook/Haplotyping/HiCBAC|Combining BAC and HiC Data]] |- style="font-size:12pt" align="center" valign="bottom" | height="15" align="left" | Use Eric's pipeline to segment SISSOR data | align="center" | January 1, 2015 | align="center" | | align="center" | [[Daniel:Notebook/Haplotyping/SISSORPipeline|SISSOR Segmentation Pipeline]] |- style="font-size:12pt" align="center" valign="bottom" | height="15" align="left" | Compare haplotypes in MHC Region | align="center" | January 1, 2015 | align="center" | | align="center" | |- style="font-size:12pt" align="center" valign="bottom" | height="15" align="left" | CPT-Seq for PGP1 | align="center" | March 1, 2016 | align="center" | | align="center" | [[Daniel:Notebook/Haplotyping/CPTSeq-PGP1|CPT-Seq Pipeline]] |}
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