DNA sequencing QC metrics

DNA sequencing QC metrics

target_dna_qc()

Examples

x = target_dna_qc()
#> Parsed with column specification:
#> cols(
#>   .default = col_double(),
#>   bamFile = col_character()
#> )
#> See spec(...) for full column specifications.
#> Parsed with column specification:
#> cols(
#>   .default = col_double(),
#>   bamFile = col_character()
#> )
#> See spec(...) for full column specifications.
#> Parsed with column specification:
#> cols(
#>   .default = col_double(),
#>   bamFile = col_character()
#> )
#> See spec(...) for full column specifications.
#> Parsed with column specification:
#> cols(
#>   .default = col_double(),
#>   bamFile = col_character()
#> )
#> See spec(...) for full column specifications.
#> Warning: The `x` argument of `as_tibble.matrix()` must have column names if `.name_repair` is omitted as of tibble 2.0.0.
#> Using compatibility `.name_repair`.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
head(x)
#> # A tibble: 6 x 46
#>   Sample Type  dataset bamFile Reads_generated Reads_mapped UNMAPPED_READS
#>   <chr>  <chr> <chr>   <chr>             <dbl>        <dbl>          <dbl>
#> 1 0A4HLD Norm… discov… 0A4HLD…       283058872    272586395       10472477
#> 2 0A4HLD Tumor discov… 0A4HLD…       170825466    166919706        3905760
#> 3 0A4HMC Norm… discov… 0A4HMC…      1972824516   1936120262       36704254
#> 4 0A4HMC Tumor discov… 0A4HMC…      2018527364   1987585279       30942085
#> 5 0A4HX8 Norm… discov… 0A4HX8…       345439442    315164331       30275111
#> 6 0A4HX8 Tumor discov… 0A4HX8…       374712362    361488204       13224158
#> # … with 39 more variables: Percentage_mapped <dbl>, Reads_duplicated <dbl>,
#> #   Percentage_duplication <dbl>, MEDIAN_INSERT_SIZE <dbl>,
#> #   MAX_INSERT_SIZE <dbl>, STANDARD_DEVIATION <dbl>, MEAN_INSERT_SIZE <dbl>,
#> #   GENOME_TERRITORY <dbl>, wgs_MEAN_COVERAGE <dbl>, wgs_SD_COVERAGE <dbl>,
#> #   wgs_MEDIAN_COVERAGE <dbl>, wgs_PCT_EXC_UNPAIRED <dbl>,
#> #   wgs_PCT_EXC_CAPPED <dbl>, wgs_PCT_EXC_TOTAL <dbl>, wgs_PCT_5X <dbl>,
#> #   wgs_PCT_10X <dbl>, wgs_PCT_20X <dbl>, wgs_PCT_50X <dbl>,
#> #   wgs_PCT_100X <dbl>, PCT_ON_BAIT <dbl>, PCT_NEAR_BAIT <dbl>,
#> #   MEAN_READ_LENGTH <dbl>, BAIT_TERRITORY <dbl>, TARGET_TERRITORY <dbl>,
#> #   MEAN_BAIT_COVERAGE <dbl>, MEAN_TARGET_COVERAGE <dbl>,
#> #   PCT_TARGET_BASES_2X <dbl>, PCT_TARGET_BASES_20X <dbl>,
#> #   PCT_TARGET_BASES_50X <dbl>, PCT_TARGET_BASES_100X <dbl>,
#> #   PCT_USABLE_BASES_ON_BAIT <dbl>, PCT_USABLE_BASES_ON_TARGET <dbl>,
#> #   FOLD_ENRICHMENT <dbl>, HS_LIBRARY_SIZE <dbl>, qMean <dbl>,
#> #   PCT_EXC_DUPE <dbl>, PCT_EXC_BASEQ <dbl>, PCT_EXC_OVERLAP <dbl>, `Average
#> #   Insert Size` <dbl>
colnames(x)
#>  [1] "Sample"                     "Type"                      
#>  [3] "dataset"                    "bamFile"                   
#>  [5] "Reads_generated"            "Reads_mapped"              
#>  [7] "UNMAPPED_READS"             "Percentage_mapped"         
#>  [9] "Reads_duplicated"           "Percentage_duplication"    
#> [11] "MEDIAN_INSERT_SIZE"         "MAX_INSERT_SIZE"           
#> [13] "STANDARD_DEVIATION"         "MEAN_INSERT_SIZE"          
#> [15] "GENOME_TERRITORY"           "wgs_MEAN_COVERAGE"         
#> [17] "wgs_SD_COVERAGE"            "wgs_MEDIAN_COVERAGE"       
#> [19] "wgs_PCT_EXC_UNPAIRED"       "wgs_PCT_EXC_CAPPED"        
#> [21] "wgs_PCT_EXC_TOTAL"          "wgs_PCT_5X"                
#> [23] "wgs_PCT_10X"                "wgs_PCT_20X"               
#> [25] "wgs_PCT_50X"                "wgs_PCT_100X"              
#> [27] "PCT_ON_BAIT"                "PCT_NEAR_BAIT"             
#> [29] "MEAN_READ_LENGTH"           "BAIT_TERRITORY"            
#> [31] "TARGET_TERRITORY"           "MEAN_BAIT_COVERAGE"        
#> [33] "MEAN_TARGET_COVERAGE"       "PCT_TARGET_BASES_2X"       
#> [35] "PCT_TARGET_BASES_20X"       "PCT_TARGET_BASES_50X"      
#> [37] "PCT_TARGET_BASES_100X"      "PCT_USABLE_BASES_ON_BAIT"  
#> [39] "PCT_USABLE_BASES_ON_TARGET" "FOLD_ENRICHMENT"           
#> [41] "HS_LIBRARY_SIZE"            "qMean"                     
#> [43] "PCT_EXC_DUPE"               "PCT_EXC_BASEQ"             
#> [45] "PCT_EXC_OVERLAP"            "Average Insert Size"       
hist(x$Percentage_duplication)
hist(x$PCT_TARGET_BASES_20X)
hist(x$PCT_NEAR_BAIT + x$PCT_ON_BAIT)