binary alignment map (bam) files (Broad Institute Inc)
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Broad Institute Inc
binary alignment map (bam) files
Binary Alignment Map (Bam) Files, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bam+binary+alignment/binary+alignment+map++bam++files/pm37407629-212-19-15
Average 90 stars, based on 1 article reviews
Binary Alignment Map (Bam) Files, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bam+binary+alignment/binary+alignment+map++bam++files/pm37407629-212-19-15
Average 90 stars, based on 1 article reviews
binary alignment map (bam) files - by Bioz Stars,
2026-10
90/100 stars
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Variant Assay:Article Title: Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group Article Snippet: For read alignment and variant calling the following software tools were used: Local Run Manager DNA Amplicon Analysis Module (3.24.1.8+), Burrow-Wheeler Aligner Maximal Exact Match (BWA-MEM) [ , ] Whole-Genome Aligner (0.7.9a-isis-1.0.2), Pisces Variant Caller (5.2.9.23), Illumina Annotation Engine (2.0.11-0- g7fb24a09), binary alignment map (BAM) Metrics (v.0.0.22), and Sequence Alignment Map (SAM) tools (0.1.19-isis-1.0.3) [ ]. Article Title: Genomic regions occupied by both RARα and VDR are involved in the convergence and cooperation of retinoid and vitamin D signaling pathways Article Snippet: For subsequent analyses, Binary Alignment Map (BAM) files were imported to the Strand NGS program (Strand Life Sciences Pvt., Bangalore, India). Article Title: Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group. Article Snippet: For read alignment and variant calling the following software tools were used: Local Run Manager DNA Amplicon Analysis Module (3.24.1.8+), Burrow-Wheeler Aligner Maximal Exact Match (BWA-MEM) [50,51] Whole-Genome Aligner (0.7.9a-isis-1.0.2), Pisces Variant Caller (5.2.9.23), Illumina Annotation Engine (2.0.11-0- g7fb24a09), binary alignment map (BAM) Metrics (v.0.0.22), and Sequence Alignment Map (SAM) tools (0.1.19-isis-1.0.3) [52]. Article Title: TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations Article Snippet: The workflow begins by taking user-provided inputs in the form of a species, list of SRA accessions, or pre-aligned Binary Alignment/Map (BAM) files for Illumina short-read sequencing data. Article Title: Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome. Article Snippet: The raw data were quality controlled, aligned and sorted by the computational pipeline at the Broad Institute to generate binary alignment map (BAM) files for tumor and blood samples separately. Article Title: Genetic Variants of the Beta-Adrenergic Receptor Pathways as Both Risk and Protective Factors for Retinopathy of Prematurity. Article Snippet: • PURPOSE: There is strong evidence that genetic factors influence retinopathy of prematurity (ROP), a neovascular eye disease.. It has been previously suggested that polymorphisms in the genes involved in β-adrenergic receptor (ADR β) pathways could protect against ROP.. Antagonists for the ADR β are actively tested in clinical trials for ROP treatment, but not without controversy and safety concerns. Article Title: Biallelic <i>BRCA</i> Loss and Homologous Recombination Deficiency in Nonbreast/Ovarian Tumors in Germline <i>BRCA1/2</i> Carriers Article Snippet: Level 1 tumor and matched normal DNA binary alignment map (BAM) files were downloaded from the Genomic Data Commons using a National Center for Biotechnology Information Genotypes and Phenotypes Database–approved protocol and underwent quality control to ensure the BRCA1/2 PGV was found at the expected heterozygous frequency in the normal BAMfile. Software:Article Title: Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group Article Snippet: For read alignment and variant calling the following software tools were used: Local Run Manager DNA Amplicon Analysis Module (3.24.1.8+), Burrow-Wheeler Aligner Maximal Exact Match (BWA-MEM) [ , ] Whole-Genome Aligner (0.7.9a-isis-1.0.2), Pisces Variant Caller (5.2.9.23), Illumina Annotation Engine (2.0.11-0- g7fb24a09), binary alignment map (BAM) Metrics (v.0.0.22), and Sequence Alignment Map (SAM) tools (0.1.19-isis-1.0.3) [ ]. Article Title: Genomic regions occupied by both RARα and VDR are involved in the convergence and cooperation of retinoid and vitamin D signaling pathways Article Snippet: For subsequent analyses, Binary Alignment Map (BAM) files were imported to the Strand NGS program (Strand Life Sciences Pvt., Bangalore, India). Article Title: Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group. Article Snippet: For read alignment and variant calling the following software tools were used: Local Run Manager DNA Amplicon Analysis Module (3.24.1.8+), Burrow-Wheeler Aligner Maximal Exact Match (BWA-MEM) [50,51] Whole-Genome Aligner (0.7.9a-isis-1.0.2), Pisces Variant Caller (5.2.9.23), Illumina Annotation Engine (2.0.11-0- g7fb24a09), binary alignment map (BAM) Metrics (v.0.0.22), and Sequence Alignment Map (SAM) tools (0.1.19-isis-1.0.3) [52]. Article Title: TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations Article Snippet: The workflow begins by taking user-provided inputs in the form of a species, list of SRA accessions, or pre-aligned Binary Alignment/Map (BAM) files for Illumina short-read sequencing data. Article Title: Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome. Article Snippet: The raw data were quality controlled, aligned and sorted by the computational pipeline at the Broad Institute to generate binary alignment map (BAM) files for tumor and blood samples separately. Article Title: Genetic Variants of the Beta-Adrenergic Receptor Pathways as Both Risk and Protective Factors for Retinopathy of Prematurity. Article Snippet: • PURPOSE: There is strong evidence that genetic factors influence retinopathy of prematurity (ROP), a neovascular eye disease.. It has been previously suggested that polymorphisms in the genes involved in β-adrenergic receptor (ADR β) pathways could protect against ROP.. Antagonists for the ADR β are actively tested in clinical trials for ROP treatment, but not without controversy and safety concerns. Article Title: Biallelic <i>BRCA</i> Loss and Homologous Recombination Deficiency in Nonbreast/Ovarian Tumors in Germline <i>BRCA1/2</i> Carriers Article Snippet: Level 1 tumor and matched normal DNA binary alignment map (BAM) files were downloaded from the Genomic Data Commons using a National Center for Biotechnology Information Genotypes and Phenotypes Database–approved protocol and underwent quality control to ensure the BRCA1/2 PGV was found at the expected heterozygous frequency in the normal BAMfile. Amplification:Article Title: Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group Article Snippet: For read alignment and variant calling the following software tools were used: Local Run Manager DNA Amplicon Analysis Module (3.24.1.8+), Burrow-Wheeler Aligner Maximal Exact Match (BWA-MEM) [ , ] Whole-Genome Aligner (0.7.9a-isis-1.0.2), Pisces Variant Caller (5.2.9.23), Illumina Annotation Engine (2.0.11-0- g7fb24a09), binary alignment map (BAM) Metrics (v.0.0.22), and Sequence Alignment Map (SAM) tools (0.1.19-isis-1.0.3) [ ]. Article Title: Genomic regions occupied by both RARα and VDR are involved in the convergence and cooperation of retinoid and vitamin D signaling pathways Article Snippet: For subsequent analyses, Binary Alignment Map (BAM) files were imported to the Strand NGS program (Strand Life Sciences Pvt., Bangalore, India). Article Title: Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group. Article Snippet: For read alignment and variant calling the following software tools were used: Local Run Manager DNA Amplicon Analysis Module (3.24.1.8+), Burrow-Wheeler Aligner Maximal Exact Match (BWA-MEM) [50,51] Whole-Genome Aligner (0.7.9a-isis-1.0.2), Pisces Variant Caller (5.2.9.23), Illumina Annotation Engine (2.0.11-0- g7fb24a09), binary alignment map (BAM) Metrics (v.0.0.22), and Sequence Alignment Map (SAM) tools (0.1.19-isis-1.0.3) [52]. Article Title: TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations Article Snippet: The workflow begins by taking user-provided inputs in the form of a species, list of SRA accessions, or pre-aligned Binary Alignment/Map (BAM) files for Illumina short-read sequencing data. Article Title: Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome. Article Snippet: The raw data were quality controlled, aligned and sorted by the computational pipeline at the Broad Institute to generate binary alignment map (BAM) files for tumor and blood samples separately. Article Title: Genetic Variants of the Beta-Adrenergic Receptor Pathways as Both Risk and Protective Factors for Retinopathy of Prematurity. Article Snippet: • PURPOSE: There is strong evidence that genetic factors influence retinopathy of prematurity (ROP), a neovascular eye disease.. It has been previously suggested that polymorphisms in the genes involved in β-adrenergic receptor (ADR β) pathways could protect against ROP.. Antagonists for the ADR β are actively tested in clinical trials for ROP treatment, but not without controversy and safety concerns. Article Title: Biallelic <i>BRCA</i> Loss and Homologous Recombination Deficiency in Nonbreast/Ovarian Tumors in Germline <i>BRCA1/2</i> Carriers Article Snippet: Level 1 tumor and matched normal DNA binary alignment map (BAM) files were downloaded from the Genomic Data Commons using a National Center for Biotechnology Information Genotypes and Phenotypes Database–approved protocol and underwent quality control to ensure the BRCA1/2 PGV was found at the expected heterozygous frequency in the normal BAMfile. Sequencing:Article Title: Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group Article Snippet: For read alignment and variant calling the following software tools were used: Local Run Manager DNA Amplicon Analysis Module (3.24.1.8+), Burrow-Wheeler Aligner Maximal Exact Match (BWA-MEM) [ , ] Whole-Genome Aligner (0.7.9a-isis-1.0.2), Pisces Variant Caller (5.2.9.23), Illumina Annotation Engine (2.0.11-0- g7fb24a09), binary alignment map (BAM) Metrics (v.0.0.22), and Sequence Alignment Map (SAM) tools (0.1.19-isis-1.0.3) [ ]. Article Title: Genomic regions occupied by both RARα and VDR are involved in the convergence and cooperation of retinoid and vitamin D signaling pathways Article Snippet: For subsequent analyses, Binary Alignment Map (BAM) files were imported to the Strand NGS program (Strand Life Sciences Pvt., Bangalore, India). Article Title: Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group. Article Snippet: For read alignment and variant calling the following software tools were used: Local Run Manager DNA Amplicon Analysis Module (3.24.1.8+), Burrow-Wheeler Aligner Maximal Exact Match (BWA-MEM) [50,51] Whole-Genome Aligner (0.7.9a-isis-1.0.2), Pisces Variant Caller (5.2.9.23), Illumina Annotation Engine (2.0.11-0- g7fb24a09), binary alignment map (BAM) Metrics (v.0.0.22), and Sequence Alignment Map (SAM) tools (0.1.19-isis-1.0.3) [52]. Article Title: TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations Article Snippet: The workflow begins by taking user-provided inputs in the form of a species, list of SRA accessions, or pre-aligned Binary Alignment/Map (BAM) files for Illumina short-read sequencing data. Article Title: Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome. Article Snippet: The raw data were quality controlled, aligned and sorted by the computational pipeline at the Broad Institute to generate binary alignment map (BAM) files for tumor and blood samples separately. Article Title: Genetic Variants of the Beta-Adrenergic Receptor Pathways as Both Risk and Protective Factors for Retinopathy of Prematurity. Article Snippet: • PURPOSE: There is strong evidence that genetic factors influence retinopathy of prematurity (ROP), a neovascular eye disease.. It has been previously suggested that polymorphisms in the genes involved in β-adrenergic receptor (ADR β) pathways could protect against ROP.. Antagonists for the ADR β are actively tested in clinical trials for ROP treatment, but not without controversy and safety concerns. Article Title: Biallelic <i>BRCA</i> Loss and Homologous Recombination Deficiency in Nonbreast/Ovarian Tumors in Germline <i>BRCA1/2</i> Carriers Article Snippet: Level 1 tumor and matched normal DNA binary alignment map (BAM) files were downloaded from the Genomic Data Commons using a National Center for Biotechnology Information Genotypes and Phenotypes Database–approved protocol and underwent quality control to ensure the BRCA1/2 PGV was found at the expected heterozygous frequency in the normal BAMfile. |