Glossary

Acronym/Term	Definition
Allele	A sequence of one or more basecalls at specific positions, that are characteristically observed together
BAI	Binary alignment index file, containing index into a given BAM file.
BAM	Binary alignment file, containing alignments of sequencing reads to a known reference genome.
CIGAR	String that denotes the sequence of matches/mismatches, insertions, deletions, and soft-clipped bases in an alignment.
Direction	Strand direction, either “forward” or “reverse”.
Fasta	Text based format for represented nucleotide sequence(s).
gVCF	Genome variant call file. This is the same format as a variant call file but includes reference and no calls. May be restricted to specific intervals.
MNV	Multi-nucleotide variation.
Picard	Industry standard toolset developed by the Broad Institute.
Reference	Allele(s) which are the same as the reference genome.
SNV	Single nucleotide variation.
SVC	The Illumina Somatic Variant Caller, Pisces.
Variant	Allele(s) which is different than the reference genome.
VCF	Variant call file.
Qscore	Phred quality score.
Wildtype	Phenotype matching the reference.