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Revision as of 10:24, 2 February 2017
, 10:24, 2 February 2017→Getting started
== Introduction ==
== Introduction ==
Main Workshop wiki page: [[SeqShop: December 2014]]
See the [[Media:LASER-tutorial.pdf|tutorial slides]] for an introduction of the LASER analysis workflow, input/output file formats, and usage of the LASER software.
See the [[Media:LASER-tutorial.pdf|tutorial slides]] for an introduction of the LASER analysis workflow, input/output file formats, and usage of the LASER software.
The main purpose of this page is to provide step-by-step command lines for using LASER to estimate ancestry of 6 targeted sequenced samples (2 HapMap trios) in a principal component space generated using genome-wide SNP data from the Human Genome Diversity Project (HGDP). The HGDP reference panel contains genotype data across 632,958 autosomal loci for 938 individuals from 53 populations worldwide.
The main purpose of this page is to provide step-by-step command lines for using LASER to estimate ancestry of 6 targeted sequenced samples (2 HapMap trios) in a principal component space generated using genome-wide SNP data from the Human Genome Diversity Project (HGDP). The HGDP reference panel contains genotype data across 632,958 autosomal loci for 938 individuals from 53 populations worldwide.
For more details about the options and usage of LASER, please read the [http://www.sph.umich.edu/csg/chaolong/LASER/LASER_Manual.pdf manual].
For more details about the options and usage of LASER, please read the [http://csg.sph.umich.edu//chaolong/LASER/LASER_Manual.pdf manual].
== LASER workflow ==
== LASER workflow ==
== Setup in person at the SeqShop Workshop ==
== Setup in person at the SeqShop Workshop ==
''This section is specifically for the SeqShop Workshop computers.''
''This section is specifically for the SeqShop Workshop computers.''
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''If you are not running during the SeqShop Workshop, please skip this section.''
''If you are not running during the SeqShop Workshop, please skip this section.''
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== Setup when running on your own outside of the SeqShop Workshop ==
== Setup when running on your own outside of the SeqShop Workshop ==
''This section is specifically for running on your own outside of the SeqShop Workshop.''
''This section is specifically for running on your own outside of the SeqShop Workshop.''
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''If you are running during the SeqShop Workshop, please skip this section.''
''If you are running during the SeqShop Workshop, please skip this section.''
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<li>Using bash (replace the paths below with the appropriate paths):</li>
<li>Using bash (replace the paths below with the appropriate paths):</li>
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:<pre>export REF=$SS/ancestry/ref export HGDP=$SS/ancestry/HGDP export BAM=$SS/ancestry/bams</pre>
:<pre>export LASER=$OUT/ancestry/LASER-2.01 export REF=$SS/ancestry/ref export HGDP=$SS/ancestry/HGDP export BAM=$SS/ancestry/BAM</pre>
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<li>Using tcsh (replace the paths below with the appropriate paths):</li>
<li>Using tcsh (replace the paths below with the appropriate paths):</li>
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:<pre>setenv REF $SS/ancestry/ref setenv HGDP $SS/ancestry/HGDP setenv BAM $SS/ancestry/bams</pre>
:<pre>setenv LASER $OUT/ancestry/LASER-2.01 setenv REF $SS/ancestry/ref setenv HGDP $SS/ancestry/HGDP setenv BAM $SS/ancestry/BAM</pre>
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Create a working directory:
Create a working directory:
mkdir $OUT/ancestry
mkdir -p $OUT/ancestry
cd $OUT/ancestry
cd $OUT/ancestry
Download and decompress software package:
Download and decompress software package:
wget http://www.sph.umich.edu/csg/chaolong/LASER/LASER-2.01.tar.gz
wget http://csg.sph.umich.edu//chaolong/LASER/LASER-2.01.tar.gz
tar xzvf LASER-2.01.tar.gz
tar xzvf LASER-2.01.tar.gz
== Preparing input files for LASER ==
== Preparing input files for LASER ==
This step uses samtools to generate pileup files from bam files.
This step uses samtools to generate pileup files from bam files.
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In person at workshop notes:
In person at workshop notes:
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Outside of the workshop notes:
Outside of the workshop notes:
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== Restarting SNP Call on your own Genome ==
== Return to Workshop Wiki Page ==
Return to main workshop wiki page: [[SeqShop: December 2014]]
