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* List of '''Sample Numbers'''
* List of '''Sample Numbers'''
**
** The following file contains three columns: [SampleID used in these analyses] [ID supplied by CSCT or Sardinia or other project] [Sequencing core ID (if different)]:
*** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330
* List of paths to '''BAMs''' used in this data freeze (Index file)
* List of paths to '''BAMs''' used in this data freeze (Index file)
* '''QC''' Summary
* '''QC''' Summary
**
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/GeneratingQCDistributions/QCStats.txt
** For a list of paths to all of the separate QPLOT files for each sample, see the file: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/GeneratingQCDistributions/QCFileListFinal.txt
* '''SNPCall''' Results (Produced with Gotcloud SNPCall and phased using Beagle4)
* '''SNPCall''' Results (Produced with Gotcloud SNPCall and phased using Beagle4)
*** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/filteringSamples/chr*/*.diff.discordance_matrix
*** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/filteringSamples/chr*/*.diff.discordance_matrix
** Overall discrepancy can be found:
** Overall discrepancy can be found:
*** '''''IN PROCESS'''''
*** '''''IN PROCESS'''''
