As the doctor gone rogue

August 16, 2015

Some benefits of clinical exome sequencing

Filed under: Uncategorized — Tags: — hypotheses @ 6:49 am

To date, clinical exome sequencing yielded around 25% diagnostic rate of unknown genetic diseases.

The number came from two recently published studies cited in Berg. JAMA 312(18), 2014.

The major concern in making the diagnosis remained the prior probability for each disease, which contributes directly to the false positive or false negative diagnosis of each specific condition. Also, genome-annotation remains a major challenge to all the scientists playing the roles in interpreting the results of these genome sequencing, whether it’s the whole genome or just an an exome.

The general questions that most patients would want to know include

  1. the diagnosis
  2. some explanations how the disease happened
  3. Anyone else in the family might be affected?
  4. Any treatment?
  5. Any future

Read more on the two cited references:

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February 20, 2014

A note on getting start with samtools on Mac OsX 10.8.5 Mountain Lion

Filed under: NGS — Tags: , , , , — hypotheses @ 9:50 pm

samtools is a handy tool for sequence alignment and mapping (http://samtools.sourceforge.net/

For more information, please refer to the original article here:

  • Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]

To get it to work on mac, I’ve decided to compile it.

First, get the sourcecode from http://sourceforge.net/projects/samtools/files/samtools/

Then, decompress the files in ~/bin

Compile it as usual

./configure
make
make install

You might need to have administrative right to write to system folder as well.

Next, we'll need to add a path to ~/.bash_profile

Include this in ~/.bash_profile to point to SAMTOOLS_HOME

export SAMTOOLS_HOME=~/bin/samtools-0.1.19
export PATH=$SAMTOOLS_HOME:$PATH
export PATH=$SAMTOOLS_HOME/bcftools/:$PATH
export PATH=$SAMTOOLS_HOME/misc/:$PATH

Now, samtools should be ready for you to use.

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