elPrep is a high-performance tool for preparing .sam/.bam/.cram files for variant calling in sequencing pipelines.It can be used as a drop-in replacement for SAMtools/Picard, and was extensively tested with different pipelines for variant analysis with GATK.
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PLoS One. 2015 Jul 16;10(7):e0132868. doi: 10.1371/journal.pone.0132868. eCollection 2015.
elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.
Herzeel C, Costanza P, Decap D, Fostier J, Reumers J