First of all I'm an undergrad summer intern and this is my first time ever working in the field of bioinformatics, so I have no idea what I am doing. I am sure I am going to misuse many words in this post. I have been instructed to construct a variant caller to detect SNPs from a genome in comparison to a single reference genome. I am using 10x genomics sequenced BAM files ( http://www.10xgenomics.com/technology). These BAM files assign barcodes to reads. Using this barcode information, I have been able to assign small reads to larger molecules (up to 700k BP).
I understand the general Bayesian methods to detect variants, such as the freeBayes variant caller ( http://arxiv.org/abs/1207.3907). So basically, I have information that a bunch of reads belong to the same molecule, and thus the same chromosome. How can I use this information to help me with detecting SNP variants. I am happy to answer any questions about what I have written, or 10x sequencing technology.
Any ideas or insight would be extremely helpful. If I would be able to speak with or message somebody about this project, I would be very grateful. I am very lost and in over my head with this projects.