My Pileup File Doesn'T Match The Documented Format? What Are These Columns?

Question

[Applet]

Hi everyone,

I'm new to Bioinformatics and I'm playing around with some existing code and I'm trying to make sense of the pileup file it's generating.

I'm using Samtools version 0.1.7 and I'm running the pileup command like this:

> samtools pileup -f [fasta file] [another file I'm not sure what it is] -c > my.pileup

My file looks like this:

2L    4043    T    T    108    0    37    27    ...........................    CCCCCCCCCCCCBCCCCCCCCCCCCCC
2L    4044    T    T    108    0    37    27    ...........................    CCCCCCCCCCCCCCCCCCCCCCCCCCC
2L    4045    T    T    81    0    37    27    .................C.........    CCCCCCCCCCCCCCCCC<CCCCCCCCC
2L    4046    C    C    108    0    37    27    ...........................    CCCCCCCCCCCCCCCCCCCCCCCCCAC

But the documentation says it will look like this:

seq1 272 T 24  ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&
seq1 273 T 23  ,.....,,.,.,...,,,.,..A <<<;<<<<<<<<<3<=<<<;<<+
seq1 274 T 23  ,.$....,,.,.,...,,,.,...    7<7;<;<<<<<<<<<=<;<;<<6
seq1 275 A 23  ,$....,,.,.,...,,,.,...^l.  <+;9*<<<<<<<<<=<<:;<<<<
seq1 276 G 22  ...T,,.,.,...,,,.,....  33;+<<7=7<<7<&<<1;<<6<
seq1 277 T 22  ....,,.,.,.C.,,,.,..G.  +7<;<<<<<<<&<=<<:;<<&<
seq1 278 G 23  ....,,.,.,...,,,.,....^k.   %38*<<;<7<<7<=<<<;<<<<<
seq1 279 C 23  A..T,,.,.,...,,,.,..... ;75&<<<<<<<<<=<<<9<<:<<

Would anyone know why there are differences? And more importantly what are the additional columns?

Answer 1

[Pierre Lindenbaum]

You have used the -c option: it changes the output format. See the (old) FAQ.

Also, pileup is deprecated you should now use mpileup