Multithreaded variant calling in elPrep 5.
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ABSTRACT:
SUBMITTER: Herzeel C
PROVIDER: S-EPMC7861424 | biostudies-literature | 2021
REPOSITORIES: biostudies-literature
Publications
Multithreaded variant calling in elPrep 5.
Herzeel Charlotte C Costanza Pascal P Decap Dries D Fostier Jan J Wuyts Roel R Verachtert Wilfried W
PloS one 20210204 2
We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and optical duplicate marking, sorting by coordinate order, base quality score recalibration, and variant calling using the haplotype caller algorithm. elPrep 5 produces identical BAM and VCF output as GATK4 while significantly reducing the runtime by p ...[more]
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