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hg38-noalt-hapmap_snps
|
public |
HapMap v3.3 SNP calls
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
|
hg38-noalt-gtf
|
public |
Ensembl GTF file distributed by Ensembl for hg38-noalt
Cleans GTF file by converting chromosome names to standard names
Uses https://github.com/dpryan79/ChromosomeMappings to remap the chromosome names
|
2025-03-25 |
|
hg38-noalt-dbsnp
|
public |
dbSNP 144: http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/
UCSFify name sed magic from: https://github.com/mmarchin/utilities/blob/master/ucscify.sh
|
2025-03-25 |
|
hg38-noalt-coverage
|
public |
Problematic and other coverage regions of interest
Low complexity regions from supplemental data of Heng Li's work on
reducing variant calling artifacts:
http://bioinformatics.oxfordjournals.org/content/30/20/2843
https://github.com/lh3/varcmp/tree/master/scripts
Centromere and other exclusion regions for SV calling from:
https://github.com/tobiasrausch/delly/blob/master/excludeTemplates/human.hg38.excl.tsv
|
2025-03-25 |
|
hg38-noalt-clinvar
|
public |
ClinVar: http://www.clinvar.com/
UCSFify name sed magic from: https://github.com/mmarchin/utilities/blob/master/ucscify.sh
|
2025-03-25 |
|
hg38-noalt-bwa
|
public |
pre-built bwa indices from NCBIs hg38 distribution with no alternative alleles
|
2025-03-25 |
|
hg38-noalt-bowtie2
|
public |
pre-build bwa indices
|
2025-03-25 |
|
hg38-noalt-1000g_snps
|
public |
1000 genomes phase 1 SNP calls
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
|
hg38-noalt-1000g_omni_snps
|
public |
1000 genomes OMNI 2.5 array calls
http://www.1000genomes.org/category/frequently-asked-questions/omni
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
|
hg38-noalt-1000g_indels
|
public |
1000 genomes phase 1 indel calls
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
|
hg38-mills_indels
|
public |
Curated training indels from Mills et al:
http://genome.cshlp.org/content/21/6/830.full
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
|
hg38-hisat2
|
public |
hisat2 (v2.0.1) reference with Ensembl release 78 exon and splicesite annotations
Derived from NCBI set with HLA and decoy alternative alleles
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/
README.md has an in depth description of how this was created
|
2025-03-25 |
|
hg38-hapmap_snps
|
public |
HapMap v3.3 SNP calls
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
|
hg38-gtf
|
public |
Ensembl GTF file distributed by Ensembl for hg38
Cleans GTF file by converting chromosome names to standard names
Uses https://github.com/dpryan79/ChromosomeMappings to remap the chromosome names
|
2025-03-25 |
|
hg38-giab-na12878-remap
|
public |
Truth sets from the Genome in a Bottle project (https://sites.stanford.edu/abms/giab)
Converted to hg38 coordinates using scripts from:
https://github.com/hbc/giab_remap_38
These are created using NCBI's remap
|
2025-03-25 |
|
hg38-giab-na12878-crossmap
|
public |
Truth sets from the Genome in a Bottle project (https://sites.stanford.edu/abms/giab)
Converted to hg38 coordinates using scripts from:
https://github.com/hbc/giab_remap_38
These are created using CrossMap with UCSC chain files.
|
2025-03-25 |
|
hg38-dream-syn4-crossmap
|
public |
Truth sets from the DREAM genomic challenge 4
https://www.synapse.org/#!Synapse:syn312572/wiki/62018
Originally retrieved from https://www.synapse.org/#!Synapse:syn2177211
and prepared with this script:
https://github.com/chapmanb/bcbio-nextgen/blob/master/scripts/utils/format_dream_truthset.py
Converted to hg38 coordinates with CrossMap:
https://github.com/hbc/giab_remap_38
|
2025-03-25 |
|
hg38-dream-syn3-crossmap
|
public |
Truth sets from the DREAM genomic challenge 3
https://www.synapse.org/#!Synapse:syn312572/wiki/62018
Originally retrieved from https://www.synapse.org/#!Synapse:syn2177211
and prepared with this script:
https://github.com/chapmanb/bcbio-nextgen/blob/master/scripts/utils/format_dream_truthset.py
Converted to hg38 coordinates with CrossMap:
https://github.com/hbc/giab_remap_38
|
2025-03-25 |
|
hg38-dbsnp
|
public |
dbSNP 144: http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/
UCSFify name sed magic from: https://github.com/mmarchin/utilities/blob/master/ucscify.sh
|
2025-03-25 |
|
hg38-coverage
|
public |
Problematic and other coverage regions of interest
Low complexity regions from supplemental data of Heng Li's work on
reducing variant calling artifacts:
http://bioinformatics.oxfordjournals.org/content/30/20/2843
https://github.com/lh3/varcmp/tree/master/scripts
Centromere and other exclusion regions for SV calling from:
https://github.com/tobiasrausch/delly/blob/master/excludeTemplates/human.hg38.excl.tsv
|
2025-03-25 |
|
hg38-clinvar
|
public |
ClinVar: http://www.clinvar.com/
UCSFify name sed magic from: https://github.com/mmarchin/utilities/blob/master/ucscify.sh
|
2025-03-25 |
|
hg38-bwa
|
public |
Full hg38/GRCh38 reference genome distributed by 1000 genomes
Derived from NCBI set with HLA and decoy alternative alleles
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/
Pre-build bwa indices
|
2025-03-25 |
|
hg38-1000g_snps
|
public |
1000 genomes phase 1 SNP calls
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
|
hg38-1000g_omni_snps
|
public |
1000 genomes OMNI 2.5 array calls
http://www.1000genomes.org/category/frequently-asked-questions/omni
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
|
hg38-1000g_indels
|
public |
1000 genomes phase 1 indel calls
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
