elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

elPrep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software architecture that allows executing preparati...

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Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines

Summary: To evaluate and compare the performance of variant calling methods and their confidence scores, comparisons between a test call set and a “gold standard” need to be carried out. Unfortunately, these comparisons are not straightforward with the current Variant Call Files (VCF), which are the standard output of most variant calling algorithms for high-throughput sequencing data. Comparis...

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Mapping whole genome shotgun sequence and variant calling in

Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these species have provided unique insights into mammalian gene function. However, the number of speci...

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Mapping whole genome shotgun sequence and variant calling in

Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these species have provided unique insights into mammalian gene function. However, the number of speci...

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Mapping whole genome shotgun sequence and variant calling in

Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these species have provided unique insights into mammalian gene function. However, the number of speci...

متن کامل

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

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