Picard sortbam
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Picard sortbam
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http://www.htslib.org/doc/samtools-sort.html
Webb26 sep. 2013 · sort (factor (q,levels=chrOrder, ordered=TRUE)) No, you don't have to use an ordered factor, as has been pointed out, but it's certainly not wrong--and it's arguably better. Factors are for this type of situation, where you have well-defined levels. See this previous question on on factor vs character. Webbbamsort reads a BAM, SAM or CRAM file, sorts it by coordinate (lexicographical by reference sequence id and position on reference sequence), query name (possibly including the HI aux tag for ordering alignments featuring the same query name), hash value computed for the query name or an aux tag value and writes the sorted file in BAM, SAM …
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WebbHistorically samtools sort also accepted a less flexible way of specifying the final and temporary output filenames: samtools sort [ -f] [ -o ] in.bam out.prefix. This has now been removed. The previous out.prefix argument (and -f option, if any) should be changed to an appropriate combination of -T PREFIX and -o FILE.
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