Hello Galaxy Biostar, For the past three weeks I've been trying to call SNPs and INDELs on my NGS samples for a summer research project. I'm a college student and all of this is new to me, but I've learned so much in these past three weeks. So far I have put my fastq files through bowtie2 on galaxy which created a sorted BAM file. I've ran QC on the fastq files and the BAM files and they have all came up in good results. I can open up the BAM files for my samples in IGV and scroll through the genome looking for mutations (I'm studying Arabidopsis Thaliana). Now for the part that I'm stuck at.... I can't find a program (that works) that will call all of the SNPs and INDELs for me. Either they don't call any INDELs at all or they miss many obvious SNPs that I can see on IGV. It's just getting very frustrating. I don't know how to run code, so doing anything outside of galaxy really isn't an option. Any help would be nice! Point me in the right direction! Is there someone who could do this step for me? Thank you galaxy community!
You will not find a program that will call ALL of the SNPs and INDELs. Each program has different biases and is prone to different types of errors. Here is a link to a paper that specifically looks at different pipelines for variant calling: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671096/
Personally, I have found that freebayes works for my purposes, but the program that works best for you will be dependent on your dataset and what exactly you are looking for.