I was recommended to use this website for information, but I cannot find a lot of information on GATK here.
I need to find the # of reads aligned to a genome. How would I go about doing that in java? This is to assess the quality of sequencing data in BAM files. I am not very familiar with any methods or implementation of it, which I cannot find on the GATK wiki. I understand that there are data traversals and data walkers, but how do I use them? Some example code in which a walker is used would be really helpful.
Thanks
I need to find the # of reads aligned to a genome. How would I go about doing that in java? This is to assess the quality of sequencing data in BAM files. I am not very familiar with any methods or implementation of it, which I cannot find on the GATK wiki. I understand that there are data traversals and data walkers, but how do I use them? Some example code in which a walker is used would be really helpful.
Thanks