Changes

From Genome Analysis Wiki
Jump to navigationJump to search

SeqShop: Calling Your Own Genome, December 2014 (view source)

Revision as of 13:34, 8 December 2014

948 bytes added ,  13:34, 8 December 2014
no edit summary
Line 20: Line 20:  
* It should now look basically the same as your normal command line.
 
* It should now look basically the same as your normal command line.
   −
;Want to log out and leave your job running?
+
; Scrolling problems when using screen?
−
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.
  −
 
  −
;How do you log back into screen tomorrow?
  −
screen -r
  −
This will resume an already running screen.
  −
* Feel free to test it out and you will see your alignment still running
  −
** Just use Ctrl-a d to detach from screen and leave your job running
  −
 
  −
; Scrolling problems?
   
: If you want to scroll and screen doesn't scroll like you normally would?
 
: If you want to scroll and screen doesn't scroll like you normally would?
 
:* Type Ctrl-a Esc and you should be able to scroll up with your mouse wheel
 
:* Type Ctrl-a Esc and you should be able to scroll up with your mouse wheel
 
:** Or at least that is what I do from my Linux machine - (sorry I'm typing this up/testing these commands from Linux and not windows, so can't test it out)
 
:** Or at least that is what I do from my Linux machine - (sorry I'm typing this up/testing these commands from Linux and not windows, so can't test it out)
   −
== Log Out ==
  −
If you have not detached from screen:
  −
Ctrl-a d
     −
exit PuTTY
+
Set these values.  Also, be sure to specify your sample name instead of SampleXX
 +
export SAMPLE=SampleXX
 +
source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
 +
 
 +
See the settings you just used:
 +
cat /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
 +
Shows you:
 +
:<code>export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud</code>
 +
:<code>export OUT=~/$SAMPLE/output</code>
 +
 
 +
 
 +
== 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 SnpCall ==
 +
 
 +
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
   −
Set these values. If you used a different path for any of these, please update here. Also, be sure to specify your sample name instead of Sample_XXXXX
+
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
   −
source /home/mktrost/seqshop/setup.2x.txt
+
</pre>
−
export SAMPLE=Sample_XXXXX
  −
export ALIGN_OUT=~/personal/output
  −
export CHR20_OUT=~/personal/output.20
  −
mkdir -p $CHR20_OUT
  −
export EXOME_OUT=~/personal/output.exome
  −
mkdir -p $EXOME_OUT
     −
ALIGN_OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately
+
== Running SnpCall ==
 +
${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
 +
* Only need the configuration & number of threads, rest is specified within the configuration.
   −
Verify that this does not give an error:
  −
ls $ALIGN_OUT/bams/${SAMPLE}.recal.bam
      
== Chromosome 20 ==
 
== Chromosome 20 ==
Line 149: Line 169:  
* --batchopts tells mosix the options to run with
 
* --batchopts tells mosix the options to run with
 
** for mosix, -j10,11,12,13 says to run on nodes 10, 11, 12, & 13 - the names of the 4 nodes on our mini-cluster
 
** for mosix, -j10,11,12,13 says to run on nodes 10, 11, 12, & 13 - the names of the 4 nodes on our mini-cluster
 +
 +
== 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
 +
 +
 +
== Logging Back in to Check Jobs ==
 +
 +
;How do you log back into screen tomorrow?
 +
screen -r
 +
This will resume an already running screen.
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12214"

Navigation menu