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| :<code>export OUT=~/$SAMPLE/output</code> | | :<code>export OUT=~/$SAMPLE/output</code> |
| | | |
− | == Step 1 (Day 1): Start SnpCall == | + | <div class="mw-collapsible" style="width:500px"> |
| + | == SnpCall Step 1 (Day 1): Start SnpCall == |
| + | <div class="mw-collapsible-content"> |
| === List of BAMs === | | === List of BAMs === |
| The list of BAMs has already been created (just 1 BAM, your sample). | | The list of BAMs has already been created (just 1 BAM, your sample). |
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| https://docs.google.com/forms/d/1n8xYxvsOq-HsabpDfGcHvwD84BYIRDx8_b-H5N3d-D8/viewform | | https://docs.google.com/forms/d/1n8xYxvsOq-HsabpDfGcHvwD84BYIRDx8_b-H5N3d-D8/viewform |
| | | |
− | == Step 2 (Day 2): Checking SnpCall == | + | </div> |
| + | </div> |
| + | |
| + | <div class="mw-collapsible" style="width:500px"> |
| + | == SnpCall Step 2 (Day 2): Checking SnpCall == |
| + | <div class="mw-collapsible-content"> |
| + | === Logging Back in to Check Jobs === |
| + | |
| + | ;How do you log back into screen tomorrow? |
| + | screen -r |
| + | This will resume an already running screen. |
| + | |
| + | == Indel Step 1 (Day 1): Start Indel Calling == |
| + | === List of BAMs === |
| + | The list of BAMs has already been created (just 1 BAM, your sample). |
| + | * But it is simply SAMPLE\tBAM_name, so easy to figure out |
| + | |
| + | cat ~/$SAMPLE/output/bam.list |
| + | |
| + | :<code>SampleXX SampleXX/output/bams/SampleXX.recal.bam</code> |
| + | * Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path). |
| + | |
| + | === Configuring Indel === |
| + | No special Configuration settings for Indel calling |
| + | cat ~/$SAMPLE/gotcloud.conf |
| + | |
| + | You will see something like this: |
| + | <pre> |
| + | # Cluster Settings |
| + | BATCH_TYPE = |
| + | BATCH_OPTS = |
| + | |
| + | OUT_DIR = Sample13/output |
| + | |
| + | # Align Settings |
| + | MAP_TYPE = BWA_MEM |
| + | BWA_THREADS = -t 24 |
| + | FASTQ_LIST = fastq.list |
| + | |
| + | # SNP Call Settings |
| + | UNIT_CHUNK = 20000000 # Chunk size of SNP calling : 20Mb |
| + | VCF_EXTRACT = /net/seqshop-server/home/mktrost/seqshop/singleSample/snpOnly.vcf.gz |
| + | MODEL_GLFSINGLE = TRUE |
| + | MODEL_SKIP_DISCOVER = FALSE |
| + | MODEL_AF_PRIOR = TRUE |
| + | |
| + | EXT_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample/ext |
| + | EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz |
| + | </pre> |
| + | |
| + | === Running Indel Calling === |
| + | Run GotCloud indel with 6 jobs running in parallel |
| + | * Why 6? |
| + | ** You want to run as many as you can. |
| + | ** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine |
| + | ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6 |
| + | * Only need the configuration & number of threads, rest is specified within the configuration. |
| + | |
| + | This will run overnight. We will check if it completed at the practical in the morning. |
| + | |
| + | === Log Out === |
| + | ;Want to log out and leave your job running? |
| + | In the screen window, type: |
| + | Ctrl-a d |
| + | (Hold down Ctrl and type 'a', let go of both and type 'd') |
| + | * This will "detach" from your screen session while your alignment continues to run. |
| + | |
| + | If you have not detached from screen: |
| + | Ctrl-a d |
| + | |
| + | exit PuTTY |
| + | |
| + | === Tuesday FEEDBACK! === |
| + | Please provide feedback on the lectures/tutorials from today: |
| + | |
| + | https://docs.google.com/forms/d/1n8xYxvsOq-HsabpDfGcHvwD84BYIRDx8_b-H5N3d-D8/viewform |
| + | </div> |
| + | </div> |
| + | |
| + | == Step 2 (Day 2): Checking Indel == |
| === Logging Back in to Check Jobs === | | === Logging Back in to Check Jobs === |
| | | |