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Revision as of 15:56, 25 August 2015
, 15:56, 25 August 2015Undo revision 13683 by Pjvh (talk) revert all changes involving `--list bam.list`
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
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genstrip_parameters.txt
genstrip_parameters.txt
This file contains the GenomeSTRiP configuration settings.
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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'''.
${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.
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.
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.
${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
