Pileup format

Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence.

This format facilitates visual display of SNP/indel calling and alignment.

It was first used by Tony Cox and Zemin Ning at the Wellcome Trust Sanger Institute, and became widely known through its implementation within the SAMtools software suite.

If present, the ASCII value of the character minus 33 gives the mapping Phred quality of each of the bases in the previous column 5.

This is similar to quality encoding in the FASTQ format.