87
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Locations of Files for Current Data Freeze of 3840 Samples
== Status as of June 2016 ==
== Status as of June 2016 ==
=== Locations of Files for Current Data Freeze of 3840 Samples===
=== Locations of Files for Current Data Freeze of 3839 Samples===
NOTICE: We identified late in the process that two of the samples (22855 and 22385) were actually the same individual. They both should be the same individual 22855. Therefore, there are 3840 sample IDs in each of the files below, but only 22855 should move on to later processes. In future data freezes with this data, these two sequencing sets should be merged into a single 22855 individual.
* List of Sample Numbers
* List of Sample Numbers
**
**
* QC for all 3840 samples
* QC Summary
**
**
* Summary of Copy Number for 3840 samples
* 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
** Individual 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
** 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:
*** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/filteringSamples/chr*/*.diff.discordance_matrix
** Overall discrepancy can be found:
*** IN PROCESS
=== What is Complete ===
=== What is Complete ===
