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09-26-2011, 03:49 PM
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#1 |
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Senior Member
Location: IL Join Date: Jul 2011
Posts: 100
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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 |
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09-26-2011, 05:35 PM
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#2 | |
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Junior Member
Location: USA Join Date: Jun 2011
Posts: 6
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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: Quote:
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