| 5 | | TODO. |
| 6 | | Suggested parties to take this up: |
| 7 | | Antoine van Kampen, Barbara van Schaik, AMC |
| | 6 | = Workflows = |
| | 7 | |
| | 8 | == Create grid directory and change permissions == |
| | 9 | |
| | 10 | [[Image(CreateGridDirectory.png)]] |
| | 11 | * Creates a directory on the LFC |
| | 12 | * Changes the permissions such that it is in-accessible to the group and others |
| | 13 | |
| | 14 | == Create a BWA index on a database == |
| | 15 | |
| | 16 | [[Image(bwaIndexDatabase.png, 50%)]] |
| | 17 | |
| | 18 | == Split fastq file == |
| | 19 | |
| | 20 | [[Image(splitFastq.png, 50%)]] |
| | 21 | |
| | 22 | == Alignment with BWA on each split file == |
| | 23 | |
| | 24 | [[Image(BWAparam.png, 50%)]] |
| | 25 | |
| | 26 | == Merge bam files == |
| | 27 | |
| | 28 | [[Image(MergeIndexSNPcall.png, 50%)]] |
| | 29 | |
| | 30 | == SNP calling with varscan, determine coverage == |
| | 31 | |
| | 32 | [[Image(Coverage_Varscan_BaseCoverage.png)]] |
