pibase - validational and comparative analysis of BAM files

http://www.ikmb.uni-kiel.de/pibase/

Essentials:
pibase_bamref	Extract information from a BAM-file and a reference sequence file and table this information into a tab-separated text file.
pibase_consensus	Infer 'best' genotypes and their 'quality' classification, and optionally merge multiple pibase_bamref files (e.g. a control panel or several runs of the same patient) into a single file.
pibase_fisherdiff	Compare two pibase_consensus files using Fisher's exact test on original data (aligned reads) rather than comparing processed data (SNP-calls or genotypes).
Annotate:
pibase_tosnpacts	Works with our unpublished annotation pipeline. Contact us if you wish us to annotate your pibase files with our annotations.
pibase_annot	Works with our unpublished annotation pipeline. Contact us if you wish us to annotate your pibase files with our annotations.
pibase_tag	Add primer region tags to a pibase_bamref, pibase_consensus, pibase_fisherdiff, or pibase_annot file.
Phylogenetics:
pibase_to_rdf	Generate rdf file (for phylogenetic network analysis) from set of pibase_fisherdiff files.
pibase_rdf_ref	Generate a reference sample file from a pibase_consensus file, prior to generating the set of pibase_fisherdiff files required for pibase_to_rdf.
pibase_chrm_to_crs	Extract Cambridge Reference Sequence (Anderson 1981) variants from reads mapped to chrM (hg18, hg19, or NCBI36).
Utilities:
pibase_to_vcf	Convert a single-sample pibase file into VCFv4.1 format.
pibase_c_to_contig	Convert pibase-contig-numbers into contig names (e.g. 25 -> chrM).
pibase_flagsnp	Flag non-reference genotypes in a pibase_consensus file as potential mismatches ("SNPs" in NGS-parlance).
pibase_diff	Compare two pibase_consensus files using (BestGen) genotypes and a (BestQual) quality threshold.
pibase_gen_from_snpacts	Works with our unpublished annotation pipeline. Contact us if you wish us to merge SNPs from SNP-callers, SNP-chips, or Sanger sequences into your pibase files for a genotype-comparison.
pibase_ref	Gets 500 flanking nucleotides of reference sequence around each coordinate (of the input list) and outputs a pseudo-FASTA file. For example for manual Sanger-sequencing primer design.