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| ** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run snpcall on your own samples. | | ** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run snpcall on your own samples. |
| *Run <code>ldrefine</code> pipeline test: | | *Run <code>ldrefine</code> pipeline test: |
− | gotcloud snpcall --test OUTPUT_DIR | + | gotcloud ldrefine --test OUTPUT_DIR |
| ** Where <code>OUTPUT_DIR</code> is the directory where you want to store the test results | | ** Where <code>OUTPUT_DIR</code> is the directory where you want to store the test results |
| ** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run ldrefine on your own samples. | | ** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run ldrefine on your own samples. |
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| *** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample. | | *** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample. |
| | | |
− | The path to the BAM List file is defaulted to the <code>outputDirectory/bam.list</code>. It can be overridden by setting <code>--bamlist</code>, <code>--bam_list</code>, or <code>--list</code> on the command-line or by setting BAM_LIST in your configuration file to the path to the BAM List File. | + | The path to the BAM List file is defaulted to the <code>outputDirectory/bam.list</code>. It can be overridden by setting <code>--bamlist</code>, <code>--bam_list</code>, or <code>--list</code> on the command-line or by setting BAM_LIST in your configuration file to the path to the BAM List File. See [[#Required_Options|Required Options]] for more information. |
| | | |
| === Reference Files === | | === Reference Files === |
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| == Variant Calling Command-line Options/Configuration Settings == | | == Variant Calling Command-line Options/Configuration Settings == |
| {{:GotCloud: Variant Calling Options}} | | {{:GotCloud: Variant Calling Options}} |
| + | |
| + | |
| + | == Use Cases & Recommended Settings == |
| + | === Single Sample Processing === |
| + | To run single sample processing we recommend adding the following settings to your configuration file: |
| + | UNIT_CHUNK = 20000000 |
| + | MODEL_GLFSINGLE = TRUE |
| + | MODEL_SKIP_DISCOVER = FALSE |
| + | MODEL_AF_PRIOR = TRUE |
| + | VCF_EXTRACT = $(REF_DIR)/snpOnly.vcf.gz |
| + | EXT = $(REF_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(REF_DIR)/chrCHR.filtered.sites.vcf.gz |
| + | |
| + | Explanation of these settings: |
| + | * <code>UNIT_CHUNK</code> - since this is only 1 sample, process larger regions at a time than default |
| + | * <code>MODEL_GLFSINGLE</code> - single sample, so model glfsingle |
| + | * <code>MODEL_SKIP_DISCOVER</code> - do not skip the variant discovery step |
| + | * <code>MODEL_AF_PRIOR</code> - use AF prior for genotyping |
| + | * <code>VCF_EXTRACT</code> - VCF file to use for extracting the site information to genotype |
| + | ** This file is included in the latest reference release: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142|hs37d5-db142]] |
| + | * <code>EXT</code> - VCF reference files to use for the external filtering |
| + | ** These files are included in the latest reference release: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142|hs37d5-db142]] |
| + | |
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