Changes

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} --list bams/bam.list

  ${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]].

** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line

** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line

** Based on <code>gotcloud.conf</code>, the GenomeSTRiP output will go in <code>$(OUT_DIR)/sv</code>

** Based on <code>gotcloud.conf</code>, the GenomeSTRiP output will go in <code>$(OUT_DIR)/sv</code>

This will take ~2-3 minutes to finish.

This will take ~2-3 minutes to finish.

The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.  

The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.  

* If running on a small machine, you may want to reduce <code>--numjobs</code> from 8 to 1.

* If running on a small machine, you may want to reduce <code>--numjobs</code> from 8 to 1.

  ${GC}/gotcloud genomestrip --run-genotype --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 8 --base-prefix ${SS} --outdir ${OUT} --list bams/bam.list

  ${GC}/gotcloud genomestrip --run-genotype --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 8 --base-prefix ${SS} --outdir ${OUT}

This will take ~3 minutes to finish.

This will take ~3 minutes to finish.

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 8 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 \

  ${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

--conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --numjobs 8 --list bams/bam.list

This will take ~1 minute to finish.

This will take ~1 minute to finish.