Cell Quality Classifier

|Feature name|Source|Description | | —-| —-|—-| |percent_duplicate_reads|picard|percentage of reads marked as PCR duplicate by MarkDuplicates| |total_mapped_reads | samtools|number of reads mapped by the bwa mem alignment algorithm | |total_duplicate_reads | samtools|number of reads marked as PCR duplicate by MarkDuplicates | |standard_deviation_insert_size| picard| read insert size standard deviation | |MSRSI_non_integerness| hmmcopy| median of segment residuals from segment integer copy number states| |MBRSI_dispersion_non_integerness| hmmcopy| median of bin residuals from segment integer copy number states| |MBRSM_dispersion| hmmcopy | median of bin residuals from segment median copy number values| |autocorrelation_hmmcopy| | autocorrelation of CNV results| |cv_hmmcopy| hmmcopy| coefficient of variation of CNV results| |mad_hmmcopy| hmmcopy| mean absolute deviation of CNV results| |total_halfiness|hmmcopy | halfiness score but without copy number state scaling| |scaled_halfiness| hmmcopy| a scaled metric to assess integer goodness of fit, described in text| |mean_state_mads| hmmcopy| the mean across all MADs of each copy number state| |mean_state_vars| hmmcopy| the mean across all variances of each copy number state| |breakpoints| hmmcopy| number of intrachromosomal breakpoints| |mean_copy| hmmcopy| mean copy number of all genomic bin segments| |state_mode| hmmcopy| the most commonly occuring copy nubmer state| |log_likelihood| hmmcopy| log-likelihood of HMMcopy CNV fit|

Percent Duplicate Reads

Calculated from the output of Mark Duplicates from picard tools. Please see mark duplicates

Formula:

UNPAIRED_READ_DUPLICATES + ((READ_PAIR_DUPLICATES + READ_PAIR_OPTICAL_DUPLICATES)*2) / (UNPAIRED_READS_EXAMINED + (READ_PAIRS_EXAMINED * 2))