Tag: hs37d5

DOI: 10.18129/B9.bioc.MafDb.gnomAD.r2.1.hs37d5   This is the development version of MafDb.gnomAD.r2.1.hs37d5; for the stable release version, see MafDb.gnomAD.r2.1.hs37d5. Minor allele frequency data from gnomAD release 2.1 for hs37d5 Bioconductor version: Development (3.18) Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.1) for the human genome version hs37d5….

Can I liftover hs37d5 to hg38 using hg19ToHg38 chain file? 1 “d” here stands for decoy sequences. They are extra short unmapped contigs. These doesn’t change the major contigs, and doesn’t affect liftover. Login before adding your answer. Traffic: 2800 users visited in the last hour Read more here: Source…

All radiocarbon dates were calibrated in OxCal 4.4 using the IntCal20 calibration curve18,19. There is no stable carbon and nitrogen isotopic evidence for any detectable input of marine or freshwater foods that would require a correction for reservoir effects. Charterhouse Warren: Archaeological context Charterhouse Warren is a natural shaft in…

DOI: 10.18129/B9.bioc.SomaticSignatures     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SomaticSignatures. Somatic Signatures Bioconductor version: 3.13 The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with…

Calculating QC Statistics Statistics: Alternative allele frequency > 0.5 sites: 337,476 Reference Overlap: 38.98 % Match: 5,762,722 Allele switch: 0 Strand flip: 0 Strand flip and allele switch: 0 A/T, C/G genotypes: 0 Filtered sites: Filter flag set: 0 Invalid alleles: 0 Multiallelic sites: 63,834 Duplicated sites: 21 NonSNP sites:…

I want to simulate variant calling of an ultra-low-coverage >0.005x bam file. I subsampled reads from the (HG02024) sample of the 1KG phase 3 dataset. My code in R to do so is the following (bam and reference are just path extensions, file is the inital bam file): cov_rate <-…

DOI: 10.18129/B9.bioc.RESOLVE     This is the development version of RESOLVE; for the stable release version, see RESOLVE. RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes Bioconductor version: Development (3.17) Cancer is a genetic disease caused by somatic mutations in genes controlling key biological…

How good is Genozip at compressing BAM files? ​ See Benchmarks. ​ Compressing a BAM, SAM or CRAM file  ​ In the rest of this page we will give examples of BAM files. Genozip is also capable of compressing SAM files, and with some limitations, CRAM files as well. ​…

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

Liftover vcf file from hs37d5 assembly to b37 assembly 0 Hello, I have a vcf file which consists of mutations that was generated using the GATK variant calling workflow. For this the hs37d5 assembly was used. The problem is, that all GAKT reference resources use the b37 assembly, and if…

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…