Scripts

User Scripts

These are scripts that you run directly that will run the Supplemental scripts

• stats_at_refpos
• runsamplesheet.sh
• runsample
• graphs.sh
• consensuses.sh
• miseq_sync
• roche_sync
• sanger_sync
• ion_sync
• rename_sample
• make_example_config

Supplemental

These are scripts that you can run manually, however, they are run automatically by the User Scripts above

• run_bwa_on_samplename
• vcf_consensus
• gen_flagstats.sh
• graphsample
• graph_mapunmap
• tagreads
• base_caller
• graph_times
• trim_reads
• ngs_filter
• fqstats
• sample_coverage

Libraries

Python Scripts/Modules that you can import to do other analysis

• ngs_mapper.run_bwa
• ngs_mapper.reads
• ngs_mapper.data
• ngs_mapper.bam
• ngs_mapper.alphabet
• ngs_mapper.stats_at_refpos
• ngs_mapper.samtools
• ngs_mapper.log

Deprecated

Scripts that are no longer used, but kept for reference in the deprecated directory

• varcaller.py
• variants.sh
• perms.sh
• gen_consensus.sh
• setup
• install.sh