Sorry to post very basic question.
I'm aligning some sanger sequences in fasta format using bowtie and then viewing using samtools. My fasta sequences cover two known SNPs that are quite common and therefore a number of the samples are heterozygous and thus have IUB codes. The bowtie sam-format output shows that the IUB coding has been replaced with the sequence now showing the variant allele. Looking at the alignment I therefore don't know which are homozygous or heterozygous for the minor allele?
Can I assume that bowtie/sam is more suited to simply SNP discovery rather than allele frequency analysis? Or does anyone know how bowtie can be set to show which are hets for the minor allele?
Many thanks.
I'm aligning some sanger sequences in fasta format using bowtie and then viewing using samtools. My fasta sequences cover two known SNPs that are quite common and therefore a number of the samples are heterozygous and thus have IUB codes. The bowtie sam-format output shows that the IUB coding has been replaced with the sequence now showing the variant allele. Looking at the alignment I therefore don't know which are homozygous or heterozygous for the minor allele?
Can I assume that bowtie/sam is more suited to simply SNP discovery rather than allele frequency analysis? Or does anyone know how bowtie can be set to show which are hets for the minor allele?
Many thanks.