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A class representing information in SAMTools pileup format
Dan MacLean ([email protected])
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 “seq2t151tGtGt36t0t99t12t.….……At:9<;;7=<<<<<” Pileup provides accessors for all columns (6 or 10 column format) and a few other useful methods
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