Upstream pipelines start from raw paired-end sequencing data as fastq files, align the reads to the reference genome and produce analysis-ready bam files for use in downstream variant calling pipelines.
Analysis-ready bam files are standard alignment files that undergo additional processing to remove duplicate reads and recalibrate base quality scores.
.. toctree:: :maxdepth: 2 upstream_GATK/index-upstream_GATK upstream_sentieon/index-upstream_sentieon