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| mills.208620indels.22.sites.bcf.csi | | mills.208620indels.22.sites.bcf.csi |
| mills_indels_hg19.22.sites.bcf | | mills_indels_hg19.22.sites.bcf |
| + | |
| + | The files special for GenomeSTRiP: |
| + | human_g1k_v37.chr22.mask.100.fasta |
| + | human_g1k_v37.chr22.mask.100.fasta.fai |
| + | humgen_g1k_v37_ploidy.chr22.map |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="mw-collapsible-content" style="width:800px"> | | <div class="mw-collapsible-content" style="width:800px"> |
| genstrip_parameters.txt | | genstrip_parameters.txt |
| + | |
| + | This file contains the GenomeSTRiP configuration settings. |
| </div> | | </div> |
| </div> | | </div> |
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| '''WAIT!!!!! DO NOT RUN THIS COMMAND, because it will take >1 hour to finish'''. | | '''WAIT!!!!! DO NOT RUN THIS COMMAND, because it will take >1 hour to finish'''. |
| | | |
− | perl ${GC}/bin/genomestrip.pl --run-metadata --conf ${SS}/gotcloud.conf --numjobs 12 --base-prefix ${SS} --outdir ${OUT} | + | ${GC}/gotcloud genomestrip --run-metadata --conf ${SS}/gotcloud.conf --numjobs 12 --base-prefix ${SS} --outdir ${OUT} |
| | | |
| Instead, let's look what the output would have looked like. | | Instead, let's look what the output would have looked like. |
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| To discover large deletions from the 62 BAMs we are using for this workshop, you can run the following command | | To discover large deletions from the 62 BAMs we are using for this workshop, you can run the following command |
| ${GC}/gotcloud genomestrip --run-discovery --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} | | ${GC}/gotcloud genomestrip --run-discovery --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} |
− | * <code>${GC}/gotcloud genomestrip -run-discovery</code> runs the GenomeSTRiP Discovery Pipeline | + | * <code>${GC}/gotcloud genomestrip --run-discovery</code> runs the GenomeSTRiP Discovery Pipeline |
| * <code>--metadata ${SS}/metadata</code> points to the pre-made metadata file as explained in the previous section, [[#Running GotCloud/GenomeSTRiP Metadata Pipeline|Running GotCloud/GenomeSTRiP Metadata Pipeline]]. | | * <code>--metadata ${SS}/metadata</code> points to the pre-made metadata file as explained in the previous section, [[#Running GotCloud/GenomeSTRiP Metadata Pipeline|Running GotCloud/GenomeSTRiP Metadata Pipeline]]. |
| * <code>--conf ${SS}/gotcloud.conf</code> points to the configuration file to use. | | * <code>--conf ${SS}/gotcloud.conf</code> points to the configuration file to use. |
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| | | |
| You can take a 3rd-party site and genotype with GenomeSTRiP. Here we take a 1000 Genomes phase 1 sites and genotype them. | | You can take a 3rd-party site and genotype with GenomeSTRiP. Here we take a 1000 Genomes phase 1 sites and genotype them. |
− | * If running on a small machine, you may want to reduce <code>--numjobs</code> from 4 to 1. | + | * If running on a small machine, you may want to reduce <code>--numjobs</code> from 8 to 1. |
− | perl ${GC}/bin/genomestrip.pl --run-thirdparty --in-vcf ${SS}/ext/1kg.phase1.chr22.36Mb.sites.vcf --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --numjobs 2 | + | ${GC}/gotcloud genomestrip --run-thirdparty --in-vcf ${SS}/ext/1kg.phase1.chr22.36Mb.sites.vcf --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --numjobs 8 |
| | | |
| This will take ~1 minute to finish. | | This will take ~1 minute to finish. |
| | | |
− | You can also check the output by running | + | You can check the output by running |
| | | |
| zless $OUT/sv/thirdparty/genotype.vcf.gz | | zless $OUT/sv/thirdparty/genotype.vcf.gz |