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Old 08-29-2011, 09:39 AM   #1
sdvie
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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:

Code:
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.
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Old 08-29-2011, 11:49 AM   #2
swbarnes2
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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.
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Old 08-30-2011, 03:08 AM   #3
sdvie
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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I am aware that pileup has been replaced by mpileup, however, I was reproducing data generated with the old pileup, when I came about this issue.

Cheers!
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