Mpileup: View The Bases That Were Involved In Making The Call

Question

[Lee Katz]

Hi, I want to use samtools mpileup because it's not deprecated, but I want to be able to perform the base calling myself. The pileup command is deprecated but shows the actual bases involved in making the call which is awesome. Is there a way to output the bases in the mpileup command so that I can make my own call? Thereby, getting the best of both worlds: not deprecated and also showing the base pileup?

Answer 1

[matted]

It will do that by default if you don't output in BCF format (that is, omit -b). It will give you:

chr10   250     N       85      A$A$A$a$AaaAAaaaaTaaaaaAaAaaaAAAaaaAaAaaaaaaaaAAaaaaaAAaAaaaaaaaAaaaaaAAaAaaAaaaaaaAaAaa^!a     hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
chr10   251     N       85      A$a$a$AAaaaaAaaaaaAaAaaaAAAaaaAaAaaaaaaaaAAaaaaaAAaAaaaaaaaAaaaaaAAaAaaAaaaaaaAaAgaa^!A^!a^!A^!a        hhhhhhhhhdhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
chr10   252     N       85      G$G$g$g$ggGgggggGgGgggGGGgggGgGggggggggGGgggggGGgGgggggggGgggggGGgGggGggggggGgGgggGgGg^!g^!g^!g hhhhhhhhhhhhhhhhhhhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhhhhhhhXhhhhhhhhhhhJhXh
chr10   253     N       83      c$c$CcccccCcCcccCCCcccCcCccccccccCCcccccCCcCcccccccCcccccCCcCccCccccccCcCcccCcCcccc^!C^!c       hhghhhhhhhhhhhhhHhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
chr10   254     N       84      T$t$t$tttTtTtttTTTtttTtTttttttttTTtttttTTtTtttttttTtttttTTtTttTttttttTtTtttTtTttttTt^!T^!T^!t   hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
chr10   255     N       83      a$a$aAaAaaaAAAaaaAaAaaaaaaaaAAaaaaaAAaAaaaaaaaAaaaaaAAaAaaAaaaaaaAaAaaaAaAaaaaAaAAa^!a^!a       hhhhhhhhhhh>hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

And if you specific the reference (with -f) it will replace matching bases with . or ,, depending on the strand:

chr10   250     A       84      .$.$.$,$.,,..,,,,T,,,,,.,.,,,...,,,.,.,,,,,,,,..,,,,,..,.,,,,,,,.,,,,,..,.,,.,,,,,,.,.,^!,      ::::AAAYYYY\\EeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhfhhhhhhMhD\\\[[BB;;=
chr10   251     A       84      .$,$,$..,,,,.,,,,,.,.,,,...,,,.,.,,,,,,,,..,,,,,..,.,,,,,,,.,,,,,..,.,,.,,,,,,.,.,,^!.^!,^!.^!, ???TTTT\\EeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhfhhhhhhPhG\\\]]EE>>>EEEE
chr10   252     G       84      .$.$,$,$,,.,,,,,.,.,,,...,,,.,.,,,,,,,,..,,,,,..,.,,,,,,,.,,,,,..,.,,.,,,,,,.,.,,.,.,^!,^!,^!,  EEEEUUEeehhhhhhhhhhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhhhhhhhXhhhhhheUUUJEEE
chr10   253     C       83      ,$,$.,,,,,.,.,,,...,,,.,.,,,,,,,,..,,,,,..,.,,,,,,,.,,,,,..,.,,.,,,,,,.,.,,,.,.,,,,^!.^!,       EEEUUeehhhhhhhhhHhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhdhheeeeUUUEE
chr10   254     T       84      .$,$,$,,,.,.,,,...,,,.,.,,,,,,,,..,,,,,..,.,,,,,,,.,,,,,..,.,,.,,,,,,.,.,,,.,.,,,,.,^!.^!.^!,   ADDIIUUUUUUUhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeUUEEE
chr10   255     A       83      ,$,$,.,.,,,...,,,.,.,,,,,,,,..,,,,,..,.,,,,,,,.,,,,,..,.,,.,,,,,,.,.,,,.,.,,,,.,..,^!,^!,       CCRRRRRRRhh>hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeQQQEE

This assumes you want to do it by parsing the pileup, like you said. I believe you can get the same information out of BCF/VCF directly.

[Lee Katz]

Perfect, thanks. This is exactly what I needed. I just did the command "samtools mpileup tmp.bam" to get the kind of output you displayed.