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Revision as of 23:22, 8 December 2014
, 23:22, 8 December 2014no edit summary
:<code>export OUT=~/$SAMPLE/output</code>
:<code>export OUT=~/$SAMPLE/output</code>
== Step 1 (Day 1): Start SnpCall ==
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== SnpCall Step 1 (Day 1): Start SnpCall ==
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=== 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).
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 ==
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== SnpCall Step 2 (Day 2): Checking SnpCall ==
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=== 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
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== Step 2 (Day 2): Checking Indel ==
=== Logging Back in to Check Jobs ===
=== Logging Back in to Check Jobs ===
