Tag: GRCH37

Bioconductor – SNPlocs.Hsapiens.dbSNP155.GRCh37 (development version)

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP155.GRCh37     This is the development version of SNPlocs.Hsapiens.dbSNP155.GRCh37; to use it, please install the devel version of Bioconductor. Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh37/hg19 assembly Bioconductor version: Development (3.16) The 929,496,192 SNPs in this package were extracted from…

Continue Reading Bioconductor – SNPlocs.Hsapiens.dbSNP155.GRCh37 (development version)

Ensembl ID mapping GRCh37 vs GRCh38

Ensembl ID mapping GRCh37 vs GRCh38 0 I currently have a large list of Ensembl protein IDs (ENSP) that are from GRCh37. I need to map these IDs to the entry name listed on the UniProt website (e.g. ‘CASPE_HUMAN’ ). I am having trouble doing this using the UniProt dataset…

Continue Reading Ensembl ID mapping GRCh37 vs GRCh38

How to modify VCF file?

Hi community, I have a question: the SNP position in vcf file is from GRCh37/hg19, I need to change the position to GRCh38. So, I used UCSC liftover to replace the hg19 pos by GRCh38 pos and deleted some SNPs, then sorted the pos and saved to a new vcf…

Continue Reading How to modify VCF file?

Obtain equivalent variant ids (chr-pos-ref-alt) for GRCh37 and GRCh38

Obtain equivalent variant ids (chr-pos-ref-alt) for GRCh37 and GRCh38 0 Hi all, I want to obtain the equivalent variant id (chr-pos-ref-alt) from GRCh38 in GRCh37. This is to deal with some variants poorly lifted over. To exemplify, see the variant gnomad.broadinstitute.org/variant/10-17838942-A-G?dataset=gnomad_r3 It has two equivalents in GRCh37. I want to…

Continue Reading Obtain equivalent variant ids (chr-pos-ref-alt) for GRCh37 and GRCh38

Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

Continue Reading Genetic and chemotherapeutic influences on germline hypermutation

On a reference pan-genome model (Part II)

12 July 2019 I wrote a blog post on a potential reference pan-genome model. I had more thoughts in my mind. I didn’t write about them because they are immature. Nonetheless, a few readers raised questions related to my immature thoughts, so I decide to add this “Part II” as…

Continue Reading On a reference pan-genome model (Part II)

Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error

Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error 0 @efernandez-22025 Last seen 1 day ago Argentina Hi I am triying to build the human index using ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz I am using Rsubread 2.4.3 an it gives me the following error //================================= Running ==================================\ || || || Check the integrity of…

Continue Reading Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error

BTG2 gene predicts poor outcome in PT-DLBCL

Introduction Primary testicular diffuse large B-cell lymphoma (PT-DLBCL) is a rare and aggressive form of mature B-cell lymphoma.1–3 PT-DLBCL was the most common type of testicular tumor in men aged over 60 and characterized by painless uni- or bilateral testicular masses with infrequent constitutional symptoms.4–6 PT-DLBCL shows significant extranodal tropism,…

Continue Reading BTG2 gene predicts poor outcome in PT-DLBCL

rs532111960 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

Continue Reading rs532111960 RefSNP Report – dbSNP

use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

Continue Reading use tcgabiolinks package to download TCGA data

rs9789283 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

Continue Reading rs9789283 RefSNP Report – dbSNP

links to Ensembl GRCh37 – gitmetadata

Open Targets Genetics reports GRCh38 coordinates but ‘External references” section points to GRCh37 (grch37.ensembl.org) rather than GRCh38 (www.ensembl.org): genetics.opentargets.org/variant/8_102432699_T_C Was this a deliberate decision (e.g. we don’t have the rsID in GRCh38 for some reason, other)? If so, we need to make this clear in the docs. If not, we…

Continue Reading links to Ensembl GRCh37 – gitmetadata

Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

Continue Reading Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

VEP issue: ERROR: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match

Describe the issue VEP give errors even my query and reference has same assembly version Command :$: ./vep -i examples/homo_sapiens_GRCh37.vcf –cache –refseq cache reference details while running install.pl ? 458 NB: Remember to use –refseq when running the VEP with this cache! downloading ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_refseq_vep_104_GRCh37.tar.gz unpacking homo_sapiens_refseq_vep_104_GRCh37.tar.gz converting cache, this may…

Continue Reading VEP issue: ERROR: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match

Failed to instantiate plugin dbNSFP in VEP

Failed to instantiate plugin dbNSFP in VEP 0 Hi Team, My VEP (version 105, installed by perl INSTALL.pl) works well. But I face some problems to use dbNSFP plugin (also installed by perl INSTALL.pl) with VEP tool. My dbNSFP version 4.2a was installed by the following code without any warning…

Continue Reading Failed to instantiate plugin dbNSFP in VEP

SNP2TFBS

SNP2TFBS Viewing variants that affect TF binding – Results – SNP identifier Chrom id (Feb 2009 GRCh37/hg19) SNP position NB. of TF factors rs1800629   dbSNP NC_000006.11 (chr6) 31543031 1 TF name  PWM score on Ref PWM score on Alt Score difference Low Score Thr High Score Thr MZF1_1-4  1024  ….

Continue Reading SNP2TFBS

Bioconductor – BSgenome.Hsapiens.UCSC.hg19

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.UCSC.hg19. Full genome sequences for Homo sapiens (UCSC version hg19) Bioconductor version: 3.2 Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. Author:…

Continue Reading Bioconductor – BSgenome.Hsapiens.UCSC.hg19

Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs

Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs 0 I have a set of 58000 SNPs for which the SNP ID is in the format of: chr:pos:effect allele:ref allele (Grch37 build), but I need to convert this to rsID where one is available for the SNP. I’ve tried using…

Continue Reading Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs

GEMINI ISSUE

Using gemini found at: /usr/local/bin/gemini /usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/config.py:61: YAMLLoadWarning: calling yaml.load() without Loader=… is deprecated, as the default Loader is unsafe. Please read msg.pyyaml.org/load for full details. config = yaml.load(in_handle) CADD scores are being loaded (to skip use:–skip-cadd). GERP per bp is being loaded (to skip use:–skip-gerp-bp). Traceback (most recent call last):…

Continue Reading GEMINI ISSUE

Gene coordinates for hg19

Gene coordinates for hg19 0 Hi, is there a list which gives for each gene its starting coordinate (chr:pos) and its ending one with respect to the hg19 reference genome? I have a list of positions on hg19 expressed as chr:pos and I have to assign each one to the…

Continue Reading Gene coordinates for hg19

Alternate nucleotide is more frequent than reference nucleotide. OMG I’m dizzy. How do I stop the twirl?

This is due to the fact that the very reference genomes that we use for re-alignment are themselves based on individuals who carry rare risk alleles. Thus, when we call variants against these genomes, we are, at many loci, comparing against rare disease risk alleles. As the best/worst example (depending…

Continue Reading Alternate nucleotide is more frequent than reference nucleotide. OMG I’m dizzy. How do I stop the twirl?

snpEFF not able to download GRCH38 ?

snpEFF not able to download GRCH38 ? 2 HI Why snpEff not able to download GRCH38 ? Always its showing error, But its work well with GRCH37 reference. Thanks for your comments. likithreddy@Curium:~/Downloads/snpEff_latest_core/snpEff$ java -jar snpEff.jar download GRCh38.76 java.lang.RuntimeException: Property: ‘GRCh38.76.genome’ not found at org.snpeff.interval.Genome.<init>(Genome.java:106) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681) at org.snpeff.snpEffect.Config.readConfig(Config.java:649) at…

Continue Reading snpEFF not able to download GRCH38 ?

Phasing with SHAPEIT

Edit June 7, 2020: The code below is for pre-phasing with SHAPEIT2. For phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs, see my answer here: A: ERROR: You must specify a valid interval for imputation using the -int argument, So, the steps are usually: pre-phasing…

Continue Reading Phasing with SHAPEIT

Picard CalculateHsMetrics perTargetCoverage for Novaseq bams

Picard CalculateHsMetrics perTargetCoverage for Novaseq bams 0 Hello, I would like to use Picard’s CalculateHsMetrics to calculate per target coverage for Novaseq bam files. It seems that the tool is not able to calculate mean/normalized coverage for Novaseq bams but works well with Hiseq bams. Novaseq bams report quality scores…

Continue Reading Picard CalculateHsMetrics perTargetCoverage for Novaseq bams

Produce PCA bi-plot for 1000 Genomes Phase III

Note1 – Previous version: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old) Note2 – this data is for hg19 / GRCh37 Note3 – GRCh38 data is available HERE The tutorial has been updated based on the 1000 Genomes Phase III imputed genotypes. The original tutorial was…

Continue Reading Produce PCA bi-plot for 1000 Genomes Phase III

UCSC liftover

UCSC liftover 2 Hi, I’m using UCSC liftover to convert hg19 to hg38. The result came out that I don’t understand. Feb. 2009 (GRCh37/hg19) → Dec. 2013 (GRCh38/hg38) – chr1:120904787 → chr1:143905854 Dec. 2013 (GRCh38/hg38) → Feb. 2009 (GRCh37/hg19) – chr1:143905854 → chr1:149400430 (I didn’t check “Allow multiple output regions”.)…

Continue Reading UCSC liftover

Bioconductor – GGtools

DOI: 10.18129/B9.bioc.GGtools     This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GGtools. software and data for analyses in genetics of gene expression Bioconductor version: 3.12 software and data for analyses in genetics of gene…

Continue Reading Bioconductor – GGtools

Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

Significance During the aging process, senescent cells secrete inflammatory factors, causing various age-related pathologies. Thus, controlling the senescence-associated secretory phenotype (SASP) can tremendously benefit human health. Although SASP seems to be induced by the alteration of chromosomal organization, its underlying mechanism remains unclear. Here, it has been revealed that noncoding…

Continue Reading Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

Need suggestions about pathogenicity prediction of gdc level 3 SNV file

Hi, I am trying to figure out which tool is most accurate in terms of pathogenicity prediction of TCGA SNVs level 3 data. TCGA offers SIFT, PolyPhen, and IMPACT scores for different kinds of mutations. SIFT, and PolyPhen cover mainly “Missense Mutation”, while IMPACT categorizes every kind of mutation into…

Continue Reading Need suggestions about pathogenicity prediction of gdc level 3 SNV file

GRCh37 GFF filter transcript isoforms by RefSeq Select tag or longest

GRCh37 GFF filter transcript isoforms by RefSeq Select tag or longest 0 Dear all, I tried to filter the “RefSeq Select” transcript isoforms in the GRCh37.p13 human genome annotation gff (GCF_000001405.25_GRCh37.p13_genomic.gff.gz). Specifically my goal is to retain for each gene a transcript isoform with a tag=RefSeq Select attribute if exists,…

Continue Reading GRCh37 GFF filter transcript isoforms by RefSeq Select tag or longest

What is the difference between GRCh37 and hs37? And hg19?

This is what I have found so far. Please correct me if I am wrong. GRCh37 w/o patches includes the primary assembly (22 autosomal, X. Y, and non-chromosomal supecontigs) and alternate scaffolds, but not a reference mitogenome. Non-chromosomal supercontigs are the unlocalized and unplaced scaffolds. The rCRS reference mitogenome in…

Continue Reading What is the difference between GRCh37 and hs37? And hg19?

Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

Continue Reading Inquiry related to vcf file and formatting

AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-referenced with ensembl.org)

Anyone know why I’m not getting ENSG ids for some of these symbols? The example below retrieves `NA` for multiple symbols, including AAED1 [whose ENSG is ENSG00000158122][1]. “` > library(AnnotationHub) > library(org.Hs.eg.db) > library(GEOquery) > temp download.file(getGEO(“GSM4430459″)@header$supplementary_file_1,temp) > genes unlink(temp) > ensids = mapIds(org.Hs.eg.db, keys=genes, column=”ENSEMBL”, keytype=”SYMBOL”, multiVals=”first”) > ensids[“AAED1”]…

Continue Reading AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-referenced with ensembl.org)