samtools (Tools for alignments in the SAM format)

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Downloads: 6213
Released: Jun 12, 2012
Updated: Oct 25, 2012 by xied75
Dev status: Beta Help Icon

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application, 572K, uploaded Oct 25, 2012 - 6213 downloads

Release Notes

This is the port of samtools from linux. The original project site is here

New Release 2012-10-25

Bug fix on bgzip.exe and bcftools.exe not able to open very large files, and the stdin/stdout (i.e. pipe) handling of bgzip.exe.

New Release 2012-06-12

1, Bug fix on bcftools.exe not taking pipe in.
2, minor bug on bcftools.exe output PV4 string with 3 digit exponential (i.e. change from e.g. 1.2e-006 to 1.2e-06).
3, samtools now able to access FTP/HTTP.
4, samtools mpileup tested.



1, of samtools.exe so many options, I only tested limited number of them, which are meaningful to my own project, (e.g. sorting 12GB bam files, etc.)

2, samtools tview WORKS

3, bcftools.exe not tested yet.

4, bgzip.exe works; razip.exe compress will throw exception, after you ignore that, you actually get the compressed file, (note: on 64 bit linux, it simply aborted)

5, open files by HTTP/FTP seems does not work.

More notes to follow. Keep checking.

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