Merge pull request genome#223 from dufeiyu/toil_compatibility

Add step to run add_bam_readcount_to_vcf_helper.py

Merge pull request genome#206 from dufeiyu/toil_compatibility

Add cle_annotated_vcf_filter step and strelka_cpu_reserved parameter

Merge pull request genome#203 from jasonwalker80/interleaved_fastq_pipe

DNA Alignment: Pipe Interleaved FASTQ