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SAMtools
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#	Item
21	Sequence Alignment/Map Format Specification The SAM/BAM Format Specification Working Group 11 May 2015 The master version of this document can be found at https://github.com/samtools/hts-specs. This printing is version b Add to Reading List Source URL: samtools.github.io Language: English - Date: 2015-06-03 15:01:36
22	Vyverman et al. BMC Bioinformatics:159 DOIs12859SOFTWAR E Open Access Add to Reading List Source URL: www.biomedcentral.com Language: English Bioinformatics Science Alfalfa Burrows–Wheeler transform SAMtools Biology DNA sequencing Molecular biology
23	Table S6: Metrics after applying the filter of MAPQ filter =>30 with samtools (a), GATK (b), Freebayes (c) and Bambino (d). a. # of SNPs # of SNP after No. of Exonic Aligner called Add to Reading List Source URL: www.ncbi.nlm.nih.gov Language: English DNA Genetic genealogy Single-nucleotide polymorphism BWA Biology Molecular biology Population genetics
24	Samtools CRAMS in support for improved compression formats Add to Reading List Source URL: medicalxpress.com Language: English - Date: 2014-12-03 07:14:03 Wellcome Trust Genomics Wellcome Trust Sanger Institute European Bioinformatics Institute Richard M. Durbin Computational genomics Genomic Standards Consortium Bioinformatics Biology Science
25	BCF2 Quick Reference (r198) In BCF2, each key in the FILTER, INFO and FORMAT fields is required to be defined in the VCF header. For each record, a key is stored as an integer which is the index of its first appearance Add to Reading List Source URL: samtools.github.io Language: English - Date: 2014-09-12 06:54:45 Programming language theory Type theory Program analysis Type system Pointer C Data types Computing Software engineering
26	The Tabix index file format Heng Li Field magic n ref format Add to Reading List Source URL: samtools.github.io Language: English - Date: 2014-09-12 06:54:45 C++ Standard Library Sequence container Bin
27	[This is a quick reference for BCF1, as historically implemented in Samtools. The BCF1 format is obsolete; BCF2 is widely implemented and recommended for use instead of this legacy format.] Field magic l seqnm seqnm Add to Reading List Source URL: samtools.github.io Language: English - Date: 2014-09-12 06:54:45 C++ String ATS Computing Software engineering Computer programming
28	The Variant Call Format (VCF) Version 4.1 Specification 17 Dec 2013 The master version of this document can be found at https://github.com/samtools/hts-specs. This printing is version c02ad4c from that repository, last Add to Reading List Source URL: samtools.github.io Language: English - Date: 2014-09-12 06:54:45 Classical genetics Population genetics Bioinformatics Genetic genealogy Variant Call Format Genotype International HapMap Project Microsatellite Allele frequency Biology Genetics Philosophy of biology
29	Comparison of The Genome Analysis Toolkit’s Unified Genotyper and SAMtools as variant callers across 84 exomes. K Hetrick, H Ling, E Pugh, S Griffith, B Craig, B Marosy, KF Doheny Center for Inherited Disease Research Add to Reading List Source URL: www.cidr.jhmi.edu Language: English - Date: 2014-05-30 09:11:58 DNA sequencing Molecular biology Biological databases Classical genetics International HapMap Project Genotype Haplotype DbSNP FASTQ format Biology Genetics Bioinformatics

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