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, 02:21, 15 November 2013
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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). |
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| = File format = | | = File format = |