Hello, I am tring to generate the consensus sequence by using command
However I found that in the output file there are a lot wild characters such as
So what is wrong?
Code:
samtools pileup -cf ref.fa aln.bam | samtools.pl pileup2fq -D100 > cns.fastq
Code:
~~~~~~~~~~~~~~~~~{~~~~~~~~o~~~~~~~~~~~~{~~~{~~~{{{x{{{~{{xfr uuurru{{xux{{{{{{{~~~{~~~~~~~f~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{c{{~x~~~~l{ ~~~~~~~~~~~~~xxxxxuuuroloooooollolfffiiifffcfffff``Mc]]]``]` ]`````````cffiifiiiiillllllilllllllill3liiiiiffffffff``````` ``]]]]]]]]]]ZZZWWWTTQQNNNNNQTTQEQKEKHEEEEEBBBEEHHHHKKQTWWWWW QTW]`fiiNllilillllliloolollrrrrrrrrrruuuux{{{{{{~~~~~~~~~~~~
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