Hi, I am a beginner to the field of Bioinformatics and have been learning it from online courses. An assignment given was to score polymorphic sites from MiSeq data (paired ends, two replicates) of 3 individuals. I used Bowtie2 to align the replicates of each individual to a reference genome using the Galaxy pipeline.Then I used the Naive variant caller available in Galaxy and retained only those sites where variants were observed. The input files were the 3 Bowtie2 outputs on the three individuals. I gave the output file obtained as input for the SnpSft variant type tool to identify SNPs, Ins, Del, Mnp etc.and the output gave me a VCF file and a log file. I used this VCF file as an input for the Variant annotator tool, which gave me the number of alleles and their frequencies. Now I wish to apply filters to separate the sites showing SNPs, sites showing indels, sites showing multiple nucleotide variants etc. However I am unable to go about doing this. Help and guidance on this task would be welcome. Sujata
