cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15120549
title: Intersected truth VCF for IMGAG validation data tumor-normal calling

description: Used commands

curl https://s3.eu-central-1.amazonaws.com/platinum-genomes/2017-1.0/hg38/small_variants/NA12877/NA12877.vcf.gz --output NA12877.vcf.gzcurl https://s3.eu-central-1.amazonaws.com/platinum-genomes/2017-1.0/hg38/small_variants/NA12878/NA12878.vcf.gz --output NA12878.vcf.gz

tabix NA12877.vcf.gztabix NA12878.vcf.gz

bcftools isec -Oz -w1 NA12878.vcf.gz NA12877.vcf.gz -p outcd outcp 0000.vcf.gz ../NA12878.unique.vcf.gzgunzip NA12878.unique.vcf.gz# remove PEDIGREE lines 29 to 41bgzip NA12878.unique.vcftabix NA12878.unique.vcf.gz

bcftools vcfisec output (README)



The sites file is also supplied in this submission.


This file was produced by vcfisec.The command line was:    bcftools isec  -Oz -w1 -p out NA12878.vcf.gz NA12877.vcf.gz

Using the following file names:out/0000.vcf.gz    for records private to    NA12878.vcf.gzout/0002.vcf.gz    for records from NA12878.vcf.gz shared by both    NA12878.vcf.gz NA12877.vcf.gz

Removed lines

##PEDIGREE=<Child=NA12877,Mother=NA12890,Father=NA12889>##PEDIGREE=<Child=NA12878,Mother=NA12892,Father=NA12891>##PEDIGREE=<Child=NA12879,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12880,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12881,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12882,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12883,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12884,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12885,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12886,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12887,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12888,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12893,Mother=NA12878,Father=NA12877>
DOI: 10.5281/zenodo.15120550
title: Intersected truth VCF for IMGAG validation data tumor-normal calling

description: Used commands

curl https://s3.eu-central-1.amazonaws.com/platinum-genomes/2017-1.0/hg38/small_variants/NA12877/NA12877.vcf.gz --output NA12877.vcf.gzcurl https://s3.eu-central-1.amazonaws.com/platinum-genomes/2017-1.0/hg38/small_variants/NA12878/NA12878.vcf.gz --output NA12878.vcf.gz

tabix NA12877.vcf.gztabix NA12878.vcf.gz

bcftools isec -Oz -w1 NA12878.vcf.gz NA12877.vcf.gz -p outcd outcp 0000.vcf.gz ../NA12878.unique.vcf.gzgunzip NA12878.unique.vcf.gz# remove PEDIGREE lines 29 to 41bgzip NA12878.unique.vcftabix NA12878.unique.vcf.gz

bcftools vcfisec output (README)



The sites file is also supplied in this submission.


This file was produced by vcfisec.The command line was:    bcftools isec  -Oz -w1 -p out NA12878.vcf.gz NA12877.vcf.gz

Using the following file names:out/0000.vcf.gz    for records private to    NA12878.vcf.gzout/0002.vcf.gz    for records from NA12878.vcf.gz shared by both    NA12878.vcf.gz NA12877.vcf.gz

Removed lines

##PEDIGREE=<Child=NA12877,Mother=NA12890,Father=NA12889>##PEDIGREE=<Child=NA12878,Mother=NA12892,Father=NA12891>##PEDIGREE=<Child=NA12879,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12880,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12881,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12882,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12883,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12884,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12885,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12886,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12887,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12888,Mother=NA12878,Father=NA12877>##PEDIGREE=<Child=NA12893,Mother=NA12878,Father=NA12877>
DOI: 10.3535/sja-kx9-2jn
title: †Diplotrypa petropolitana Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zeq-2ey-vm2
title: †Dianulites petropolitanus Dybowski, 1877 ()

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/3pe-r7x-wvc
title: †Diplotrypa petropolitana Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/my6-jsh-1gm
title: †Diplotrypa petropolitana Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/w6x-jaz-z91
title: †Dianulites petropolitanus Dybowski, 1877 ()

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8ez-tee-xp9
title: Pseudoasaphus globifrons Eichwald

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8jq-q2g-grp
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/edx-4h0-82s
title: †Endoceras J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/z2j-fhw-se9
title: Pseudoasaphus globifrons Eichwald

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hya-dgj-06h
title: †Pollicina crassitesta Koken, 1897

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sx0-745-x9x
title: †Phymatopleuridae Batten, 1956

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/3qr-tps-pda
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9e8-5cw-00p
title: Animalia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/axk-81h-c78
title: †Pollicina crassitesta Koken, 1897

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/y0l-c39-5a6
title: Bryozoa

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ylx-4h6-5h5
title: Conularia pectinata Holm

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/3kj-lq1-4bs
title: Animalia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xeg-s6c-ajk
title: Conularia cancellata Sandberger

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mt3-qgx-h95
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/s6l-p9f-jwp
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/n11-5l7-8cd
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/y4r-547-f35
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9zh-9y9-5ax
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.15468/dl.27zjmy
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phocoena spinipinnis Burmeister, 1865",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 102 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010512-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/02b-qfx-smd
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/r7g-xvy-rab
title: †Endoceras J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4c9-9q3-0q4
title: †Siphonotreta Verneuil, 1845

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mrn-1se-b38
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/0mn-nj9-3zm
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9jm-el0-x0m
title: †Endoceras J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/06d-gk3-1m2
title: Conularia sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tka-stv-s32
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4fw-fg0-4zs
title: Conularia sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/m1x-bjc-8rn
title: Conularia sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g1e-he0-2d9
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hjp-j7h-gxc
title: †Asaphidae

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/92p-6l7-fme
title: †Endoceras J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9jq-j46-p5g
title: Conularia sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/6dt-2q5-acb
title: Megalaspis

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/t1a-4yv-w31
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bzk-hgv-3n0
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fcy-y83-wc5
title: †Bellerophon Montfort, 1808

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ncs-g4c-mw2
title: Conularia sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/6wj-4tk-8qj
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rm9-y1s-xpj
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/br7-f8j-srq
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ttt-b7t-q3z
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/j4b-1r5-nqv
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xdn-w9m-053
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5av-ea2-bdl
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x4q-9bv-vh3
title: Megistaspis

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5nw-ygn-4p1
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5zb-7bm-1dn
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.13145/bacdive104520.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104521.20230509.8.1
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104521.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104522.20230509.8.1
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0096573.10fu
title: SH0096573.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive104522.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104523.20230509.8.1
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0096574.10fu
title: SH0096574.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive104523.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104524.20230509.8.1
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0096575.10fu
title: SH0096575.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive104524.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104525.20230509.8.1
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0096576.10fu
title: SH0096576.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive104525.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104526.20230509.8.1
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104526.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0096577.10fu
title: SH0096577.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive104527.20230509.8.1
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104527.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0096578.10fu
title: SH0096578.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive104528.20230509.8.1
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive104528.20251217.10
title: Nocardioides sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0096579.10fu
title: SH0096579.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.