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Old 08-29-2011, 09:39 AM   #1
Location: Spain

Join Date: Jul 2010
Posts: 68
Default duplicate entries in pileup file?

When greping for positions of interest, I noticed that my pileup file seems to contain a number of lines that repeat chromosome number and position, like this:

chr11	67048294	T	T	93	0	60	25	,$,$..,,,,,,,,,,,,,,,,,,,,,-2gc	EEOPPPMTT_]<ETNT3,=>%.7/!	~~~~~~~~~~~~~~~~~~~~~~~~~
chr11	67048294	*	*/*	37	0	60	25	*	-GC	24	1	0	0	0
From a pileup of a total of 15980465 lines, I get 10346 not-unique positions (chr + position).
Is this normal? If yes, why does this happen? And if not, what might be the reason?

Many thanks in advance for your comments.
sdvie is offline   Reply With Quote
Old 08-29-2011, 11:49 AM   #2
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Location: San Diego

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That's absolutely normal behavior for pileup when there's an indel in one of the reads.

Pileup has been deprecated for a long time now. Use mpileup instead.
swbarnes2 is offline   Reply With Quote
Old 08-30-2011, 03:08 AM   #3
Location: Spain

Join Date: Jul 2010
Posts: 68

Thanks, that is good to know.

I am aware that pileup has been replaced by mpileup, however, I was reproducing data generated with the old pileup, when I came about this issue.

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