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** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/SNPINDEL/beagle4/beagle4_chr*/beagle4/chr*/chr*.filtered.PASS.beagled.vcf.gz
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/SNPINDEL/beagle4/beagle4_chr*/beagle4/chr*/chr*.filtered.PASS.beagled.vcf.gz
* mtDNA Copy Number Summary
* '''mtDNA Copy Number''' Summary
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/MTDNA_COPYNUMBER/Coverage_IncludingUnpairedReads/sardiniaCopyNumber_include.txt
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/MTDNA_COPYNUMBER/Coverage_IncludingUnpairedReads/sardiniaCopyNumber_include.txt
** By sample copy number results by sample can be found: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/MTDNA_COPYNUMBER/Coverage_IncludingUnpairedReads/*.CopyNumber.noRand.500000.*.txt
** By sample copy number results by sample can be found: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/MTDNA_COPYNUMBER/Coverage_IncludingUnpairedReads/*.CopyNumber.noRand.500000.*.txt
* Discrepancy Figures
* '''Filtering Samples''': Discrepancy Figures
** We compared chip data from previous work to the sequencing data produced now in hopes of identifying which samples have reliable sequencing data. This comparison was done for each chromosome separately and then combined into an overall discrepancy figure. Only 3189 of the 3840 samples had
** We compared chip data from previous work to the sequencing data produced now in hopes of identifying which samples have reliable sequencing data. This comparison was done for each chromosome separately and then combined into an overall discrepancy figure. Only 3189 of the 3840 samples had
** By chromosome discrepancy figures can be found:
** By chromosome discrepancy figures can be found:
*** IN PROCESS
*** IN PROCESS
* Sample Name Conversion
* '''Sample Name Conversion'''
** The CSCT samples had two different names.... a numeric and an alphanumeric. The conversion key can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/SampleNameChanges.txt
** The CSCT samples had two different names.... a numeric and an alphanumeric. The conversion key can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/SampleNameChanges.txt
