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* '''Filtering Samples''': 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 (3188 of 3839 if you throw out sample with two sets of data) 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 (3188 of 3839 if you throw out sample with two sets of data) had chip data.
** By chromosome discrepancy figures can be found:
** By chromosome discrepancy figures for each sample can be found:
*** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/filteringSamples/chr*/*.diff.discordance_matrix
*** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/filteringSamples/chr*/*.diff.discordance_matrix
** By chromosome discrepancy figures for all samples in ones file can be found:
*** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/filteringSamples/chr*/all.discordance.summary.txt
=== What is Complete ===
=== What is Complete ===
