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LASER

2,611 bytes added, 01:21, 15 November 2013
Estimate ancestries of sequence samples
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== Interpret LASER outputs ==
 
Upon successfully launching LASER command line as above, the output messages should be similar to below:
 
===================================================================
==== LASER: Locating Ancestry from SEquencing Reads ====
==== Version 1.0 | (c) Chaolong Wang 2013 ====
====================================================================
Started at: Fri Nov 15 01:05:48 2013
 
938 individuals are detected in the GENO_FILE.
632958 loci are detected in the GENO_FILE.
1 individuals are detected in the SEQ_FILE.
632958 loci are detected in the SEQ_FILE.
938 individuals are detected in the COORD_FILE.
100 PCs are detected in the COORD_FILE.
 
Parameter values used in execution:
-------------------------------------------------
GENO_FILE (-g)resource/HGDP/HGDP_938.geno
SEQ_FILE (-s)pileup2seq/test.seq
COORD_FILE (-c)resource/HGDP/HGDP_938.RefPC.coord
OUT_PREFIX (-o)test
DIM (-k)2
MIN_LOCI (-l)100
SEQ_ERR (-e)0.01
FIRST_IND (-x)1
LAST_IND (-y)1
REPS (-r)1
OUTPUT_REPS (-R)0
CHECK_FORMAT (-fmt)10
CHECK_COVERAGE (-cov)0
PCA_MODE (-pca)0
-------------------------------------------------
 
Fri Nov 15 01:05:50 2013
Checking data format ...
GENO_FILE: OK.
SEQ_FILE: OK.
COORD_FILE: OK.
 
Fri Nov 15 01:06:01 2013
Reading reference genotypes ...
 
Fri Nov 15 01:09:15 2013
Reading reference PCA coordinates ...
 
Fri Nov 15 01:09:15 2013
Analyzing sequence samples ...
Results for the sequence samples are output to 'test.SeqPC.coord'.
 
Finished at: Fri Nov 15 01:09:21 2013
====================================================================
 
The ancestry of input samples are store in the file '''test.SeqPC.coord''', which content is shown below:
 
popID indivID L1 Ci t PC1 PC2
NA12878.chrom22 NA12878.chrom22 1601 0.00858193 0.977243 31.522 224.098
 
The ancestry coordinates for NA12878 samples are given in PC1 (31.522) and PC2 (224.098).
 
It is recommended to visualize this results with HGDP reference samples whose coordinates are given in file: resource/HGDP/HGDP_938.RefPC.coord
 
In our manuscript, an example figure is shown:
 
[[File:LASER paper Figure 2.png|thumb|center|alt=LASER example outputs as in Figure 2|400px|LASER Outputs]]
 
In this figure, 238 individuals were randomly selected from the total 938 HGDP samples as the testing set (colored symbols),
and the remaining 700 HGDP individuals were used as the reference panel (gray symbols).
= File format =
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