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formated table in docs
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nilesh-tawari committed Sep 8, 2017
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Expand Up @@ -93,49 +93,49 @@ Default config file
| Tool name | QC metrics | Chart type implemented in default JSON (config file) |
+==================+===================================+===============================================================================================+
| FastQC | FastQC_percent_gc | time_series_with_mean_and_stdev |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | FastQC_total_sequences | time_series_with_mean_and_stdev |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | FastQC_percent_duplicates | time_series_with_mean_and_stdev |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | FastQC_percent_fails | time_series_with_mean_and_stdev |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | FastQC_avg_sequence_length | time_series_with_mean_and_stdev |
+==================+===================================+===============================================================================================+
+------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
| QualiMap | QualiMap_30_x_pc | time_series_with_mean_and_stdev |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | QualiMap_percentage_aligned | time_series_with_mean_and_stdev |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | QualiMap_avg_gc | time_series_with_mean_and_stdev (if FastQC_percent_gc is present this plot is omitted |
| | | to avoid duplication) |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | QualiMap_mapped_reads | time_series_with_mean_and_stdev |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | QualiMap_median_coverage | time_series_with_mean_and_stdev |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | QualiMap_total_reads | time_series_with_mean_and_stdev (if FastQC_total_sequences is present this plot is omitted |
| | | to avoid duplication) |
+==================+===================================+===============================================================================================+
+------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
| Bamtools | Bamtools_mapped_reads_pct | time_series_with_mean_and_stdev (if QualiMap_mapped_reads is present this plot is |
| | | omitted to avoid duplication) |
+==================+===================================+===============================================================================================+ |
+------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
| Samtools | SamtoolsFlagstat_mapped_passed | time_series_with_mean_and_stdev (if QualiMap_percentage_aligned is present this plot is |
| | | omitted to avoid duplication) |
+==================+===================================+===============================================================================================+
+------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
| Bcftools | BcftoolsStats_number_of_MNPs | time_series_with_box_whisker_plot |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | BcftoolsStats_number_of_SNPs | time_series_with_box_whisker_plot |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | Bcftools_Stats_number_of_indels | time_series_with_box_whisker_plot |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | BcftoolsStats_number_of_records | time_series_with_box_whisker_plot |
| +===================================+===============================================================================================+
| +-----------------------------------+-----------------------------------------------------------------------------------------------+
| | BcftoolsStats_tstv | time_series_with_mean_and_stdev |
+==================+===================================+===============================================================================================+
+------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
| Peddy | Peddy_error | time_series_with_percentage_category (Default category: True) |
+==================+===================================+===============================================================================================+
+------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
| Any other tool | Columns with numeric data | time_series_with_mean_and_stdev |
+==================+===================================+===============================================================================================+
+------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+

Below is an example of default ChronQC config file generated in examples/multiqc_example_2::

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