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139 bytes added
, 12:39, 27 June 2016
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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 |
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| * List of paths to '''BAMs''' used in this data freeze (Index file) | | * List of paths to '''BAMs''' used in this data freeze (Index file) |
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| * '''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 |
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| * '''SNPCall''' Results (Produced with Gotcloud SNPCall and phased using Beagle4) | | * '''SNPCall''' Results (Produced with Gotcloud SNPCall and phased using Beagle4) |
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| *** /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'''''
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− | * '''Sample Name Conversion'''
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− | ** The CSCT samples had two different names.... a numeric and an alphanumeric. The conversion key can be found here:
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− | ***/net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/SampleNameChanges.txt
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− | ** The Sardinia samples had a Sardinia ID and a Sequencing Core ID. The conversion key can be found here:
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| *** '''''IN PROCESS''''' | | *** '''''IN PROCESS''''' |
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