I am new to samtools, IGV display and NGS in general. I have a two part question.
Part 1-
I would like to know how to interpret the output from "samtools mpileup" command. For example, in the attached txt file, column 5 has symbols like:
1- "^]," what does this denote?
2- "t" or "T" what is the difference between lower case and upper case?
3- What is "-C"?
4- why is "." or "," is used?
and so on.
Is there a comprehensive list where I can find all such information. Samtools FAQ has limited information. Any help is appreciated.
(a text file is attached herein that I am trying to interpret)
Part 2-
Is there a samtools script or easily available script that can parse the information and tell us the allele frequency / total number of A,T,G, C at each mapped position. An icon displays frequency when mouse is moved over mapped position. It would be helpful if I can extract the information from the command line .. what IGV tools function / application would be used for this.
Thanks in advance.
Part 1-
I would like to know how to interpret the output from "samtools mpileup" command. For example, in the attached txt file, column 5 has symbols like:
1- "^]," what does this denote?
2- "t" or "T" what is the difference between lower case and upper case?
3- What is "-C"?
4- why is "." or "," is used?
and so on.
Is there a comprehensive list where I can find all such information. Samtools FAQ has limited information. Any help is appreciated.
(a text file is attached herein that I am trying to interpret)
Part 2-
Is there a samtools script or easily available script that can parse the information and tell us the allele frequency / total number of A,T,G, C at each mapped position. An icon displays frequency when mouse is moved over mapped position. It would be helpful if I can extract the information from the command line .. what IGV tools function / application would be used for this.
Thanks in advance.
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