From Genome Analysis Wiki
Jump to navigationJump to search
472 bytes added
, 12:25, 6 July 2016
Line 98: |
Line 98: |
| **# 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''' |