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Reference mitochondrial DNA in GRCh37
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Imputing allele frequency into GWAS summary statistics
written by newbie problems •I have a summary statistic file which has the the following columns Column Description ID_37 Variant ID (GRCh37) Chromosome Chromosome number Position_b37 Position GRCh37 Other_allele …
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difference in the content of a tsv and bigwig file
written by Jamie Watson •I have downloaded both the tsv file and bigwig file for CADD scores. However, upon inspection these two files contain different information. For example a …
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Using vcfanno to annotate VCF file with CADD1.6 "tsv.gz" files
written by NGSCanBioinf •Hello, I am trying to use vcfanno tool to annotate my query VCF file with the CADD v1.6 files that I have installed. These files …
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mitochondrial DNA in vcf for haplogrep2
written by biosolHi everyone, I'm trying to analyse mitochondrial data from human samples, which I have stored in a `vcf`file. I've tried running `Haplogrep2` (both cmd and …
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Which GRCh37 version to use from snpEff databases for BAMs mapped with GRCh37-lite?
written by CHANG •Does anyone know which version of GRCh37 to use from snpEff databases to annotate VCF files generated from BAMS mapped with GRCh37-lite. (https://browser.cghub.ucsc.edu/help/assemblies/) > GRCh37-lite …
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Ensembl GRCh37 DAS returning GRCh38 results
written by Drei •The URL for the Ensemb GRCh37 DAS seems to be returning GRCh38 results. Is the GRCh37 DAS still in existence somewhere? For example, http://www.ensembl.org/das/Homo_sapiens.GRCh37.reference/sequence?segment=1:100000,110000 gives …
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Cuffmerge Is Looking For Contig Fasta Files That I Do Not Have!
written by jobinv<p>I downloaded the full Homo_sapiens_Ensembl_GRCh37.tar.gz file from <a href='http://cufflinks.cbcb.umd.edu/igenomes.html'>iGenomes</a> (huge file, 17 GB, but contains everything I've needed otherwise for my tuxedo suite, from genomes …
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Decoy In Reference Assembly
written by Sangwoo Kim •<p>I am using 1000 Genomes data with my new project. When I am inspecting the reference assembly they have been using, I found it contains …
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Complete Mitochondrial Sequence And Y-Chromosome Snp Data From Hapmap And Hgdp Populations
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