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Old 09-26-2011, 03:49 PM   #1
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Location: IL

Join Date: Jul 2011
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Default output info from samtools pileup?

When I piled up an alignment by this command, I received the result in the bottom. What does each column mean? I know "chr_2 5554123" is a SNP.

samtools pileup -c -f ../../ssahaSNP_result/Sorbil.fasta test.bam > test.full.pileup

chr_2 5554119 t T 30 0 60 1 . R
chr_2 5554120 t T 30 0 60 1 . P
chr_2 5554121 t T 30 0 60 1 . A
chr_2 5554122 g G 30 0 60 1 . A
chr_2 5554123 t C 0 2 60 1 C A
chr_2 5554124 a A 30 0 60 1 . X
shuang is offline   Reply With Quote
Old 09-26-2011, 05:35 PM   #2
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Hi shuang,

You can find more information about the pileup command, its input and output, etc. here.

You have used the consensus ("-c") option, which will call a consensus base according to the MAQ model for each base.

There is more information about each of these columns here:

"When consensus calling is switched on, pileup command will insert the consensus base, consensus quality, SNP quality and maximum mapping quality of the reads covering the sites between the `reference base' and the `read bases' columns."
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