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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 ]
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 ]
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]
^ (caret) marks the start of a read segment and the ASCII of the character following `^' minus 33 gives the mapping quality $ (dollar) marks the end of a read segment * (asterisk) is a placeholder for a deleted base in a multiple basepair deletion that was mentioned in a previous line by the - [0-9] + [ACGTNacgtn] + notation
The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects.
Even when using data-sort-type=number in the column header, text in front of a number in any cell breaks numerical sorting of that cell. Text after a number is not a problem if the sort order of a column is specified by using data-sort-type=number. Leading zeroes are not necessary for numerical sorting of a column.
In most cases, an index is used to quickly locate the data records from which the required data is read. In other words, the index is only used to locate data records in the table and not to return data. A covering index is a special case where the index itself contains the required data fields and can answer the required data. Consider the ...
SAM (file format) or Sequence Alignment Map, a data format used in bioinformatics; Sam (text editor) SAM Coupé, an 8-bit British home computer; Microsoft Sam, a voice for the screen reader in Windows 2000 and XP; SAM, a New Zealand chatbot that discuss politics; SAM Lock Tool, better known as Syskey; Sequential access memory