Question: Imitate Pileup Format
0
gravatar for Lee Katz
5.6 years ago by
Lee Katz2.9k
Atlanta, GA
Lee Katz2.9k wrote:

Hi, I am fixing a script that uses an older version of samtools. I just want to fix the system calls to samtools. In the script, they call samtools pileup, which produces this format (first 50 lines below). How do I imitate the output with samtools mpileup? The original command was

samtools pileup -cf tmp.fasta tmp.sorted.bam

Thank you!

1  1   A  N      0    0    0   17  ^W,^W.^W,^W.^W.^W.^W.^W,^W.^W,^W.^W.^W.^W.^W,^W.^W.                    !!!!!!!!!!!!!!!!!
1  2   C  C      39   0    54  17  ,.,....,.,....,..                                                      !!11!5!!!!!!!/!!!
1  3   A  A      39   0    54  17  ,.,....,.,....,..                                                      !!==!>!!!!!!!=!!!
1  4   T  T      39   0    54  17  ,.,....,.,....,..                                                      !!AA!A!!!!!!!A!!!
1  5   T  T      42   0    54  18  ,.,....,.,....,..^W.                                                   !!IH!I!!!!!!!I!!!E
1  6   C  C      42   0    54  18  ,.,....,.,....,...                                                     !!HH!I!!!!!!!I!!!I
1  7   T  T      42   0    54  18  ,.,....,.,....,...                                                     !!GH!I!!!!!!!I!!!I
1  8   T  T      42   0    54  18  ,.,....,.,....,...                                                     !!HH!I!!!!!!!I!!!I
1  9   T  T      42   0    54  18  ,.,....,.,....,...                                                     !!IH!I!!!!!!!I!!!I
1  10  G  G      42   0    54  18  ,.,....,.,....,...                                                     !!IH!I!!!!!!!I!!!I
1  11  T  T      45   0    54  19  ,.,....,.,....,...^W.                                                  !!IH!I!!!!!!!I!!!IE
1  12  A  A      45   0    54  19  ,.,....,.,....,....                                                    !!HH!I!!!!!!!I!!!II
1  13  A  A      48   0    54  20  ,.,....,.,....,....^W.                                                 !!IH!I!!!!!!!I!!!IIE
1  14  T  T      48   0    54  20  ,.,....,.,....,.....                                                   !!IH!I!!!!!!!I!!!III
1  15  A  A      51   0    54  21  ,.,....,.,....,.....^W,                                                !!IH!I!!!!!!!I!!!IIID
1  16  T  T      54   0    54  22  ,.,....,.,....,.....,^W,                                               !!IH!I!!!!!!!H!!!IIIIE
1  17  G  G      54   0    54  22  ,.,....,.,....,.....,,                                                 !!IH!I!!!!!!!G!!!IIIII
1  18  A  A      54   0    54  22  ,.,....,.,....,.....,,                                                 !!IH!I!!!!!!!I!!!IIIII
1  19  A  A      57   0    54  23  ,.,....,.,....,.....,,^W.                                              !!IH!H!!!!!!!I!!!IIIII>
1  20  A  A      57   0    54  23  ,.,....,.,....,.....,,.                                                !!IH!H!!!!!!!I!!!IIIII>
1  21  G  G      57   0    54  23  ,.,....,.,....,.....,,.                                                !!IH!I!!!!!!!I!!!IIIIII
1  22  A  A      60   0    54  24  ,.,....,.,....,.....,,.^W,                                             !!IH!B!!!!!!!I!!!IIIIIIE
1  23  T  T      60   0    54  24  ,.,....,.,....,.....,,.,                                               !!IH!I!!!!!!!I!!!IIIHIII
1  24  T  T      60   0    54  24  ,.,....,.,....,.....,,.,                                               !!IH!I!!!!!!!I!!!IIIIIII
1  25  G  G      60   0    54  24  ,.,....,.,....,.....,,.,                                               !!IH!I!!!!!!!G!!!IIIIIII
1  26  T  T      63   0    54  25  ,.,....,.,....,.....,,.,^W.                                            !!IH!I!!!!!!!I!!!IIIIIII
1  27  G  G      66   0    54  26  ,.,....$,.,....,.....,,.,.^W.                                          !!IH!I!!!!!!!I!!!IIIIIII
1  28  A  A      66   0    54  25  ,.,...,.,....,$..$...,,.,..                                            !!IH!I!!!!!!I!!!IIIIIIII
1  29  A  A      66   0    54  23  ,.,...,.,........,,.,..                                                !!IG!I!!!!!!D!IIIIIIIII
1  30  G  G      66   0    54  23  ,+1t.,+1t...,+1t.,+1t...$.....,+1t,+1t.,+1t..                          !!IH!G!!!!!!H!IIIIIIIII
1  30  *  +T/+T  107  799  54  23  +T                                                                     *
samtools mpileup pileup • 1.7k views
ADD COMMENTlink modified 5.6 years ago by polarise380 • written 5.6 years ago by Lee Katz2.9k

I don't find your question clear. What do you mean by 'imitate'?

ADD REPLYlink written 5.6 years ago by polarise380

I would like to run "samtools mpileup" instead of "samtools pileup." However, the output format differs. My question is, how can I use mpileup options to generate the same format?

Maybe there are options in the other tools like bcftools or vcfutils.pl to generate this format.

ADD REPLYlink written 5.6 years ago by Lee Katz2.9k
2
gravatar for polarise
5.6 years ago by
polarise380
Galway, Ireland
polarise380 wrote:

I think the best option is to build an old version of samtools that has pileup still function.

From the samtools repository on github:

Beta Release 0.1.17 (6 July, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

With the maturity of `mpileup' and the lack of update in the `pileup' command,
the `pileup' command is now formally dropped. Most of the pileup functionality,
such as outputting mapping quality and read positions, have been added
`mpileup'.

I would, therefore, suggest that you download and install version 0.1.16 then generate your pileup from that.

ADD COMMENTlink written 5.6 years ago by polarise380

this is actually a great solution - one that is obvious once stated - but easily overlooked while looking for an answer

ADD REPLYlink written 5.6 years ago by Istvan Albert ♦♦ 79k

Annoying, but true. I will try this when I get into work tomorrow (yay for Labor Day!)

ADD REPLYlink written 5.6 years ago by Lee Katz2.9k
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