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New Pileup Output

The pileup output description is different than the output I am getting now. Could anyone help me with a definition of each column? http://samtools.sourceforge.net/pileup.shtml

This is a line from my output. It has additional columns when compared against the original description.

1  621 T    G 159   159 36   74 g$g$gggggGGgggggggGGggGGGGgGGgGggGGgGGgggGGgggGGgggGGggGggGgGgGgGggGggggGGgG  !!!!***A:2223222:32238:8273232237522532222222322222922222322222222233322'!
samtools pileup format
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updated by Sean Davis Sean Davis • written by Lee Katz Lee Katz

strange, which program did you use?

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written by Russh Russh

I used the pileup command. I think that Sean Davis answered my question.

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written by Lee Katz Lee Katz

1 answer

See here:

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

Note the section under pileup where there are more details given about the extra columns. Also, note the pileup is deprecated and will be soon dropped from samtools, so consider switching to mpileup for variant calling.

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written by Sean Davis Sean Davis

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