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Old 08-03-2011, 03:30 AM   #1
Location: Finland

Join Date: Nov 2009
Posts: 19
Default pileup file format

Hi all,

I'm trying to interpret the (m)?pileup file format with regarding to the indels. The documentation says that the indels have pattern [+-][0-9]+[ACGTNacgtn]+. After looking at the format it would seem that at least . or , before the pattern is part of it.

<chr> <pos> C 7 ,,-3aga,,-3aga,-3aga.-3AGA.

Seems to follow that theory pretty well. However then I also have

<chr> <pos> T 15 ,+1g,+1g,+1g,+1g,+1g,+1g,+1g,+1g,+1g,+1g,+1gc+1g,+1g,+1g,+1g

Which does not as the one pair of +1g has been separated with 'c'. How should I interpret that?

I'm using samtools mpileup version 0.1.16, command line:
mpileup -f $GENOME -l position_list.txt -ABQ0 -d 100000 $d/alignment-sorted.bam
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