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samtools sort -m 5000000 unsorted_in.bam sorted_out Read the specified unsorted_in.bam as input, sort it in blocks up to 5 million k (5 Gb) [ units verification needed ] and write output to a series of bam files named sorted_out.0000.bam , sorted_out.0001.bam , etc., where all bam 0 reads come before any bam 1 read, etc. [ verification needed ]
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4]
The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is present.
www.htslib.org /doc /samtools-mpileup.html Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP /indel calling and alignment.
The body of VCF follows the header, and is tab separated into 8 mandatory columns and an unlimited number of optional columns that may be used to record other information about the sample(s). When additional columns are used, the first optional column is used to describe the format of the data in the columns that follow.
Indexes can be created using one or more columns of a database table, providing the basis for both rapid random lookups and efficient access of ordered records. An index is a copy of selected columns of data, from a table, that is designed to enable very efficient search. An index normally includes a "key" or direct link to the original row of ...
In the tables below, all columns sort correctly. The wikitext for the first entry in each table in the first row is shown in the table header. Note: None of the table columns use the data-sort-type= modifier. Using data-sort-type= can sometimes break sorting when used with the template.
A simple lexicographical sort can divide the index size by 9 and make indexes several times faster. [19] The larger the table, the more important it is to sort the rows. Reshuffling techniques have also been proposed to achieve the same results of sorting when indexing streaming data. [14]