Supporting data for "16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model"
Dataset type: Software
Data released on June 16, 2017
Luo R; Schatz MC; Salzberg SL (2017): Supporting data for "16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model" GigaScience Database. https://doi.org/10.5524/100316
16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy for calling indels as compared to the GATK HaplotypeCaller. 16GT is available at https://github.com/aquaskyline/16GT.
Additional details
Read the peer-reviewed publication(s):
- Luo, R., Schatz, M. C., & Salzberg, S. L. (2017). 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model. GigaScience, 6(7). https://doi.org/10.1093/gigascience/gix045 (PubMed:28637275)
Additional information:
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Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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Readme | TEXT | 1.55 kB | 2017-06-13 | MD5 checksum: bcdfaf881fa591b3f73eae89814be06b |
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Archival copy of the 16GT software, downloaded 10-Jun-2017, from Github Repo https://github.com/aquaskyline/16GT please visit GitHub for most recent updates. | GitHub archive | zip | 1.36 MB | 2017-06-13 | ||||
NA12878 BWA-MEM alignment | Alignments | BAM | 116.14 GB | 2017-06-13 | MD5 checksum: fbd3764bc51f271b885df8fe38647d22 |
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NA12878 GIAB-2.18 truth dataset | Alignments | UNKNOWN | 24.50 MB | 2017-06-13 | ||||
NA12878 GIAB-2.18 truth dataset | Sequence variants | VCF | 327.25 MB | 2017-06-13 | ||||
Variant identified using 16GT | Sequence variants | VCF | 2.26 GB | 2017-06-13 | MD5 checksum: 0f30ad82d4957e32249120dc3c27ff74 |
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Variant identified using GATK UnifiedGenotyper | Sequence variants | VCF | 1.35 GB | 2017-06-13 | MD5 checksum: 0dd0707728e5a7737a5ef8b0f7396c1d |
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Variant identified using GATK HaplotypeCaller | Sequence variants | VCF | 1.22 GB | 2017-06-13 | MD5 checksum: e7e1fd9e26edc9096d65b59292001063 |
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Variant identified using Freebayes | Sequence variants | VCF | 1.97 GB | 2017-06-13 | MD5 checksum: c636b74a5c3a425da8074fcd147e50fe |
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Variant identified using Fermikit | Sequence variants | VCF | 279.01 MB | 2017-06-13 | MD5 checksum: b65e1144ad9bb0158847471094111558 |
Code Ocean:
Date | Action |
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June 14, 2017 | Dataset publish |
October 2, 2017 | Manuscript Link added : 10.1093/gigascience/gix045 |
November 9, 2022 | Manuscript Link updated : 10.1093/gigascience/gix045 |