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Revision as of 10:24, 2 February 2017
, 10:24, 2 February 2017→Getting started
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 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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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
