Hi!
I'm using samtools and maq to find SNP in illumina files.
From MAQ, i have a file .snp (by maq cns2snp) very comprehensible, with a columns that represents the position, 1st-2nd and 3rd calls, the Phred qualities etc...
By samtools I generated a pileup file and a snp file (from samtools.pl varFilter) that is, for me, more complicated and more difficult to manage by a script perl! Could you know some method to convert these samtools files in an output more easy?
Thanx!
Bye bye,
ME
I'm using samtools and maq to find SNP in illumina files.
From MAQ, i have a file .snp (by maq cns2snp) very comprehensible, with a columns that represents the position, 1st-2nd and 3rd calls, the Phred qualities etc...
By samtools I generated a pileup file and a snp file (from samtools.pl varFilter) that is, for me, more complicated and more difficult to manage by a script perl! Could you know some method to convert these samtools files in an output more easy?
Thanx!
Bye bye,
ME