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**# If reasonable predictive power/R^2, use the prediction model to estimate the non-reference concordance amongst the 651 samples that do not have chip data. Also use the prediction model to estimate the non-reference concordance among the 3,188 samples that do have chip data.
**# If reasonable predictive power/R^2, use the prediction model to estimate the non-reference concordance amongst the 651 samples that do not have chip data. Also use the prediction model to estimate the non-reference concordance among the 3,188 samples that do have chip data.
**# Set a cut-off for 'good' versus 'bad' samples based on the estimated non-reference concordance and use it to filter samples.
**# Set a cut-off for 'good' versus 'bad' samples based on the estimated non-reference concordance and use it to filter samples.
** NOTE: The number of positions for which the chip data give 0/0 and sequencing gives 0/0, chip data gives 0/0 and sequencing gives 0/1, chip data gives 0/0 and sequencing gives 1/1, chip gives 0/1 and sequencing gives 0/0, etc. etc. BY chromosome can be found in the files /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/filteringSamples/chr*/all.discordance.summary.txt. These can be used to calculate overall non-reference concordance across all chromosomes.
* '''Mitochondrial Depth Analysis'''
* '''Mitochondrial Depth Analysis'''
* '''Telomere Length Analysis'''
* '''Telomere Length Analysis'''
