I'm running sam_gatk_coverage_to_bed on individual sample_interval_summary DoC output from GATK to get coverage within the CLAMMS windows. However the results seem to point to a bug in the code.
This is my first line of input for instance:
Target total_coverage average_coverage CDH360_total_cvg CDH360_mean_cvg CDH360_granular_Q1 CDH360_granular_median CDH360_granularQ3 CDH360%_above_15
1:14643-14882 19118 79.66 19118 79.66 71 82 88 100.0
And this is my first line of output after running sam_gatk_coverage_to_bed:
1 14642 14882 -14882
It seems like the script read in the first column and split it into three components, with the end interval position reported as coverage. Are there any workarounds?
I'm running sam_gatk_coverage_to_bed on individual sample_interval_summary DoC output from GATK to get coverage within the CLAMMS windows. However the results seem to point to a bug in the code.
This is my first line of input for instance: Target total_coverage average_coverage CDH360_total_cvg CDH360_mean_cvg CDH360_granular_Q1 CDH360_granular_median CDH360_granularQ3 CDH360%_above_15 1:14643-14882 19118 79.66 19118 79.66 71 82 88 100.0
And this is my first line of output after running sam_gatk_coverage_to_bed: 1 14642 14882 -14882
It seems like the script read in the first column and split it into three components, with the end interval position reported as coverage. Are there any workarounds?
Thanks