Tweet
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
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