I am working with small enriched viral genomes assembled using Bowtie2 from Illumina paired end reads. I have been looking at papers carrying out similar work and have come across something which may be useful for my work but the authors use the Qiagen CLC genomics workbench for data analysis which I do not have access to and it is expensive to buy access.
Is there a bcftools flag which can be used to call variants based on their presence on a set number of forward and reverse reads (i.e. must appear in at least 10 forward and 10 reverse reads to be called)? Or a percentage frequency (i.e. >2% of reads)? I have read the manual several times but cannot seem to find a solution.
If not is there another variant caller you could recommend please? I am planning to try varscan this morning
Thanks in anticipation
