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 *
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.
this is actually a great solution - one that is obvious once stated - but easily overlooked while looking for an answer
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I don't find your question clear. What do you mean by 'imitate'?
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.