ngsane
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BauerLab
Analysis Framework for Biological Data from High Throughput Experiments
I am trying to up this Image on my local by referring this [link](https://github.com/BauerLab/ngsane/wiki/How-to-use-the-virtual-machine). Please let me know how to do this ec2-create-instance-export-task command on "[Export the EC2 image as...
SamVar
Samtools variant calling is not working anymore with samtools 1.1 [bam_rmdup_core] processing reference 16... Samtools-htslib-API: bam_get_library() not yet implemented /apps/gi/ngsane/devel_db//mods/samSNPs.sh: line 97: 1358176 Aborted samtools rmdup $f $OUTDIR/${n/bam/drm.bam} This is...
There is several possibilities to reduce the footprint of bam files that we should consider as an option in the mapping mods. http://blastedbio.blogspot.com.au/2012/03/bam-verus-cram-07.html Alternatively / additional the cram tools may...
Using node-local storage speeds up IO heavy tasks significantly on SGE/PBS systems. The Trinity mods make use of this, however as a list of commands is intrinsically being generated by...
java -jar CreateSequenceDictionary.jar R= Homo_sapiens_assembly18.fasta O= Homo_sapiens_assembly18.dict - See more at: http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference#sthash.nxPJSckY.dpuf
I thought it might be nice to have a counter next to or after the checkpoints in the log files. I think this might interesting for anxious people like me...