samtools pileup output file

charlie_sequencing · 02-10-2011, 12:54 PM

Hey guys, I am using the command line "samtools pileup -cv -f ref_genome snp.sorted.bam" trying to get SNP information between RNA-Seq data and reference genome. The output file has ten columns, which I've no idea for most of them. Here are some of the output:
Group1.1 225532 T G 0 3 60 1 g B
Group1.2 1381414 C Y 0 3 60 1 T$ B
Group1.3 589260 A R 0 3 60 1 ^~g B

From what I can tell so far, the 1st column is the scaffold id and the 2nd is the scaffold coordinate where SNP occurs between the scaffold and the RNA-Seq read. Anyone has previous experiences? Thanks so much!

csoong · 02-10-2011, 01:51 PM

"pileup up is deprecated, use mpileup." (just trying to be Heng Li, heehee)
However, I remember galaxy has good docs on those fields if the manual wasn't clear for some reason.

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02-10-2011, 12:54 PM	#1
charlie_sequencing Member Location: US Join Date: Jan 2011 Posts: 13	samtools pileup output file Hey guys, I am using the command line "samtools pileup -cv -f ref_genome snp.sorted.bam" trying to get SNP information between RNA-Seq data and reference genome. The output file has ten columns, which I've no idea for most of them. Here are some of the output: Group1.1 225532 T G 0 3 60 1 g B Group1.2 1381414 C Y 0 3 60 1 T$ B Group1.3 589260 A R 0 3 60 1 ^~g B From what I can tell so far, the 1st column is the scaffold id and the 2nd is the scaffold coordinate where SNP occurs between the scaffold and the RNA-Seq read. Anyone has previous experiences? Thanks so much!

02-10-2011, 01:51 PM	#2
csoong Member Location: Connecticut Join Date: Jun 2009 Posts: 74	"pileup up is deprecated, use mpileup." (just trying to be Heng Li, heehee) However, I remember galaxy has good docs on those fields if the manual wasn't clear for some reason.