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Revision as of 22:47, 18 May 2015
, 22:47, 18 May 2015→Tuesday - Start INDEL Calling
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== Tuesday - Start INDEL Calling ==
== Tuesday - Start SNP Calling ==
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=== Setup ===
=== Setup Screen ===
The indel & snpcall pipelines will run overnight, but you'll want to log out.
The snpcall pipeline will run overnight, but you'll want to log out.
; How do I leave something running on the server even if I log out?
; How do I leave something running on the server even if I log out?
: One solution is screen!
: One solution is screen!
* It should now look basically the same as your normal command line.
* It should now look basically the same as your normal command line.
=== Setup Variables ===
Set these values. Also, be sure to specify your sample name instead of SampleXX
Set these values. Also, be sure to specify your sample name instead of SampleXX
export SAMPLE=SampleXX
export SAMPLE=SampleXX
or
export SAMPLE=NA12878
export GC=~/seqshop/gotcloud
export OUT=~/$SAMPLE/output
=== List of BAMs ===
=== List of BAMs ===
=== Configuring Indel ===
=== Configuring Indel ===
No special Configuration settings for Indel calling
No special Configuration settings for SNP calling
cat ~/$SAMPLE/gotcloud.conf
cat ~/$SAMPLE/gotcloud.conf
You will see something like this:
You will see this:
<pre>
<pre>
# Cluster Settings
# References
SS_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample
REF_DIR = $(SS_DIR)/ref/gotcloud.ref/
######### ALIGNMENT ########
# Align Settings
MAP_TYPE = BWA_MEM
MAP_TYPE = BWA_MEM
FASTQ_LIST = fastq.list
FASTQ_LIST = fastq.list
BATCH_TYPE =
BATCH_OPTS =
BWA_THREADS = -t 6
# SNP Call Settings
# SNP Call Settings
UNIT_CHUNK = 20000000 # Chunk size of SNP calling : 20Mb
UNIT_CHUNK = 20000000 # Chunk size of SNP calling : 20Mb
VCF_EXTRACT = /net/seqshop-server/home/mktrost/seqshop/singleSample/snpOnly.vcf.gz
VCF_EXTRACT = $(SS_DIR)/snpOnly.vcf.gz
MODEL_GLFSINGLE = TRUE
MODEL_GLFSINGLE = TRUE
MODEL_SKIP_DISCOVER = FALSE
MODEL_SKIP_DISCOVER = FALSE
MODEL_AF_PRIOR = TRUE
MODEL_AF_PRIOR = TRUE
EXT_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample/ext
EXT_DIR = $(SS_DIR)/ext
EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz
EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz
</pre>
</pre>
=== Running Indel Calling ===
=== Running SNP Calling ===
Run GotCloud indel with 6 jobs running in parallel
Run GotCloud snpcall with 8 jobs running in parallel
* Why 6?
* Why 8?
** You want to run as many as you can.
** 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
** 2-3 of you on the machine - 3*8 = 24 jobs will be running in parallel on that machine
${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6
${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 8 --outdir $OUT
* Only need the configuration & number of threads, rest is specified within the configuration.
* Only need the configuration & number of threads, rest is specified within the configuration.
