61
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Analysis of Structural Variation Practical, May 2015 (view source)
Revision as of 18:29, 24 August 2015
, 18:29, 24 August 2015→Running GotCloud/GenomeSTRiP Genotyping Pipeline: add `--list bams/bam.list` to the next gotcloud command
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}
${GC}/gotcloud genomestrip --run-genotype --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 8 --base-prefix ${SS} --outdir ${OUT} --list bams/bam.list
This will take ~3 minutes to finish.
This will take ~3 minutes to finish.
