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Old 03-28-2011, 07:39 AM   #1
labmtl
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Location: mtl

Join Date: Mar 2011
Posts: 2
Default interpretation insertion/deletion file SAMTOOL

Hello, I am new on the website and i would like to know if someone could help me with the interpretation of some results. I did not find enough information on the following inks:

http://samtools.sourceforge.net/pileup.shtml


http://samtools.sourceforge.net/cns0.shtml

I am looking for insertion deletion. Here are the example of 2 samples.

sample1 56 * */+CTT 87 87 37 9 * =+CTT 7 2 0 0 0
sample2 56 * =+CTT/+CTT 25 1291 37 21 =+CTT * 18 3 0 0 0

For sample 1, I understand that there are 7 reads on 9 that agree with the insertion of CTT at position 56 while 3 did not.
For samples 2 I understand that there are 18 reads on 21 that agree with the insertion of CTT at position 56 while 3 did not.
I do not inderstand what is the difference between "*/+CTT" and "=+CTT/+CTT"
Moreover i do not understand why in sample 1, in the column 9 there is a "*" and then in column 10 it is written "=+CTT", while for sample 2 , in column 9 it is written "=+CTT" and then in column 10 "*".
I would really appreciate if someone could help me, thank you so much
Best regards
Labmtl
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