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Reference mitochondrial DNA in GRCh37
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Imputing allele frequency into GWAS summary statistics
written by newbie problems 0I 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
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Using vcfanno to annotate VCF file with CADD1.6 "tsv.gz" files
written by NGSCanBioinf 1Hello, 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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Which GRCh37 version to use from snpEff databases for BAMs mapped with GRCh37-lite?
written by CHANG 4Does 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 5The 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 112<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 44<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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