Changes

How-to/SNP detection

106 bytes added, 15:37, 13 September 2011

→‎samtools

=== samtools ===

[[samtools]] using the ~~pilepup or~~ mpileup ~~pipeline~~command

http://samtools.sourceforge.net/mpileup.shtml

~~This thread here describes some potential problems that occur when using~~ '''samtools pileup''' (without the ~~BAQ parameter. (In effect it recommends to turn it off, if one uses e.g. BWA that finds indels.http://seqanswers.com/forums/showthread~~'''m''') is deprecated and has been removed in recent SAMtools versions.~~php?t=11965~~

[http://seqanswers.com/forums/showthread.php?t=11965 A SEQanswers forum thread] describes some potential problems that occur when using the BAQ parameter. (In effect it recommends to turn it off, if one uses e.g. BWA that finds indels.

=== SOAPsnp ===

Mmartin

294

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Changes

How-to/SNP detection

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