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gather metrics sh
jprofijt edited this page Feb 20, 2020
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The gathermetrics script is responsible for grouping all available data from the data storage into a few single files.
Script usage:
./gatherMetrics.sh -d projectsDirectory -o outputfile.ziprun the script once to generate a config with all options disabled.
| Config value | Discription |
|---|---|
| ISMETRICS | When set to 1, will tell the script to include the insert size metrics in the results |
| HSMETRICS | When set to 1, will tell the script to include the hs metrics in the results |
| ASMETRICS | When set to 1, will tell the script to include alignment summary metrics in the results |
| FLMETRICS | When set to 1, will tell the script to include flagstat metrics in the results |
| GCBMETRICS | When set to 1, will tell the script to include gc bias metrics in the results |
| QBCMETRICS | When set to 1, will tell the script to include quality by cycle metrics in the results |
| QDMETRICS | When set to 1, will tell the script to include quality distribution metrics in the results |
| BIMETRICS | When set to 1, will tell the script to include bam index stats in the results |