Pileup

A class representing information in SAMTools pileup format

Pileup is described at sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output. Briefly (when you invoke pileup with the -c option):

• 1 reference sequence name
• 2 reference coordinate
• (3) reference base, or `*’ for an indel line
• (4) genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example, */+A, -A/* or +CC/-C. There is no difference between */+A or +A/*.
• (5) Phred-scaled likelihood that the genotype is wrong, which is also called `consensus quality’.
• (6) Phred-scaled likelihood that the genotype is identical to the reference, which is also called `SNP quality’. Suppose the reference base is A and in alignment we see 17 G and 3 A. We will get a low consensus quality because it is difficult to distinguish an A/G heterozygote from a G/G homozygote. We will get a high SNP quality, though, because the evidence of a SNP is very strong.
• (7) root mean square (RMS) mapping quality
• 8 # reads covering the position
• 9 read bases at a SNP line (check the manual page for more information); the 1st indel allele otherwise
• 10 base quality at a SNP line; the 2nd indel allele otherwise
• (11) indel line only: # reads directly supporting the 1st indel allele
• (12) indel line only: # reads directly supporting the 2nd indel allele
• (13) indel line only: # reads supporting a third indel allele

If pileup is invoked without `-c’, indel lines and columns between 3 and 7 inclusive will not be outputted.

NB mpileup uses the 6 column output format eg "seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<" Pileup provides accessors for all columns (6 or 10 column format) and a few other useful methods