#IDI broad scripts This archive is miscellaneous vcf/sam/etc scripts I've found useful. They are provided here in case anybody else does too. They come with the usual warnings and caveats. As time goes by many of them will become out of date, or generally just stop working.

If run without any variables, all scripts in here should give a brief overview of the script and an example command line. running, eg, python myScriptName.py --help should give you details of individual options

various vcf-mangling and reporting scripts. All python scripts are py2.7 unless otherwise stated

• copyAnnotationToVCF.py
• blockSummariseVCF.py

unfinished, use-once, or generally hacky scripts. All the caveats above and then a thousand more.

• getSNPFlank.py - parse flanking seq from positions and fasta file