Overview of the PING pipeline.

The PING pipeline processes KIR targeted sequencing data to determine KIR gene copy number and allele genotypes through a series of modules. First, KIR aligned reads are filtered through an alignment to a set of KIR haplotypes in PING extractor. Second, copy number of KIR genes are determined through an exhaustive alignment to a diverse set of KIR sequences in PING copy. Finally, PING allele performs a series of alignments to determine the most congruent KIR genotype, which informs a final round of alignment and genotype determination. Additionally, PING reports any identified novel SNPs and new alleles (SNP combinations not found in any described KIR allele sequence).