Changes between Version 11 and Version 12 of WikiStart

Timestamp:

Apr 4, 2013, 3:37:05 PM (10 years ago)

Author:

r.straver@…

Comment:

--

WikiStart

@@ -60 +60 @@
 python countgc.py hg19.fasta gccountperbin.pickle
 }}}
+This takes quite a few minutes as the implementation was not focused on speed, rather on quick functionality. As you rarely have to do this step this shouldn't really be a problem.
 
 === Convert BAM to PICKLE ===
@@ -66 +67 @@
 /path/to/samtools view ex_sample.bam | python consam.py /path/to/ex_sample.pickle
 }}}
+This step is required for every test and reference sample used.
 
 === Creating a Reference Table ===
@@ -72 +74 @@
 python newref.py /path/to/refdir/ /path/to/gccountperbin.pickle /path/to/reftable.pickle
 }}}
-This step may take several minutes, mostly dependent on the amount of reference samples you provided.
+This step may take several minutes, mostly dependent on the amount of reference samples you provided. Due to the design of WISECONDOR, the more reference samples available the merrier. Even adding extremely low coverage samples (i.e. 0.03 times coverage) may improve reliability of the WISECONDOR. As these samples are only used to build a reference, any healthy whole genome sample that was produced in the same manner as the samples you would like to test will most likely do fine; male, female, pregnant, non-pregnant, different lanes, different times, different coverages, just make sure it is run on the same machine and prepared the same way, then everything should be fine. This also means that, if done right, no additional reference samples need to be sequenced for testing at some point as the reference samples made previously provide enough information.
+We suggest using at least 16 samples to provide enough information although increasing this amount is definitely a good idea.
 
 === Testing A Sample ===
@@ -79 +82 @@
 python test.py /path/to/ex_sample.pickle /path/to/gccountperbin.pickle /path/to/reftable.pickle /path/to/ex_sample.plot > /path/to/ex_sample.result
 }}}
+Output formatting is a bit confusing at this point and may improve over time.
 
 === Tweaking and Fine-Tuning ===