Hi everyone, I am using "(samtools mpileup -f ref_fasta_file bam_file > mpileup_output) >& mpileup_output.errors &" to generate mpile output.
According to the pileup format specification http://samtools.sourceforge.net/pileup.shtml, "At the read base column (Column 5 from the left), a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand". However, I got some results where greater than sign ">" and less than sign "<" were found in the read base column. Has anyone met with similar problems when dealing with mpileup output?
Thanks!
These are two output lines that I 've got:
Group1.1 329483 T 262 >>><>>>>>>>>>><>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><>>>>>>>>>>>>>>><<>..<<<<<<<<>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<><<<<<<>>>>>><><>>><>>>>>>>>>>>>>>>>>>>>>>>>.>>>>>><>>.<<<>>>>>>>>>>>>>>>>>>>>>><><<<<<<<<<<<<<<<<<<<<<<<<<<<>>>.,, e^`f_c^BYb`b]dfddb^Y`bccb_dbdecfd[Bddbd^cdafcabdedY`^dedfbeYdc__feddaca\ffec\fffffffff^ddd\a\accbTdYedBeafddffffefffeffffafffffeffeefffdfe^eBffffff`dfdfffaf^bedfafcfefabeeedfcaedfddedfefeadecdfadeddfdcfdd\fefcfdfdfffeefdfddfefdffdffdefecf^`afffdeffffeffefdeeffde
Group1.1 329484 G 262 >>><>>>>>>>>>><>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><>>>>>>>>>>>>>>><<>..<<<<<<<<>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<><<<<<<>>>>>><><>>><>>>>>>>>>>>>>>>>>>>>>>>>.>>>>>><>>.<<<>>>>>>>>>>>>>>>>>>>>>><><<<<<<<<<<<<<<<<<<<<<<<<<<<>>>.,, e^`f_c^BYb`b]dfddb^Y`bccb_dbdecfd[Bddbd^cdafcabdedY`^dedfbeYdc__feddaca\ffef_fffffffff^ddd\a\accbTdYedBeafddffffefffeffffafffffeffeefffdfe^eBffffff`dfdfffaf^bedfafcfefabeeedfcaedfddedfefeadecdfadeddfdcfdd\fefcfdfdfffeefdfddfefdffdffdefecf^`afffdeffffeffefdeeffdd
According to the pileup format specification http://samtools.sourceforge.net/pileup.shtml, "At the read base column (Column 5 from the left), a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand". However, I got some results where greater than sign ">" and less than sign "<" were found in the read base column. Has anyone met with similar problems when dealing with mpileup output?
Thanks!
These are two output lines that I 've got:
Group1.1 329483 T 262 >>><>>>>>>>>>><>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><>>>>>>>>>>>>>>><<>..<<<<<<<<>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<><<<<<<>>>>>><><>>><>>>>>>>>>>>>>>>>>>>>>>>>.>>>>>><>>.<<<>>>>>>>>>>>>>>>>>>>>>><><<<<<<<<<<<<<<<<<<<<<<<<<<<>>>.,, e^`f_c^BYb`b]dfddb^Y`bccb_dbdecfd[Bddbd^cdafcabdedY`^dedfbeYdc__feddaca\ffec\fffffffff^ddd\a\accbTdYedBeafddffffefffeffffafffffeffeefffdfe^eBffffff`dfdfffaf^bedfafcfefabeeedfcaedfddedfefeadecdfadeddfdcfdd\fefcfdfdfffeefdfddfefdffdffdefecf^`afffdeffffeffefdeeffde
Group1.1 329484 G 262 >>><>>>>>>>>>><>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><>>>>>>>>>>>>>>><<>..<<<<<<<<>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<><<<<<<>>>>>><><>>><>>>>>>>>>>>>>>>>>>>>>>>>.>>>>>><>>.<<<>>>>>>>>>>>>>>>>>>>>>><><<<<<<<<<<<<<<<<<<<<<<<<<<<>>>.,, e^`f_c^BYb`b]dfddb^Y`bccb_dbdecfd[Bddbd^cdafcabdedY`^dedfbeYdc__feddaca\ffef_fffffffff^ddd\a\accbTdYedBeafddffffefffeffffafffffeffeefffdfe^eBffffff`dfdfffaf^bedfafcfefabeeedfcaedfddedfefeadecdfadeddfdcfdd\fefcfdfdfffeefdfddfefdffdffdefecf^`afffdeffffeffefdeeffdd
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