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Old 10-24-2012, 02:48 PM   #1
Location: paris

Join Date: Oct 2009
Posts: 86
Default Some confused from samtools mpileup.

When I run samtools with follow parameters:

samtools mpileup -C50 -Q25 -q1 -l %s -f %s %s

I got a output as follow:

21 34124586 G 38 ,,,,AAA,AAAAa..,,,aaa.AaA,,A,,aaaaaaaA

From samtools manual:

"At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a ’>’ or ’<’ for a reference skip, ‘ACGTN’ for a mismatch on the forward strand and ‘acgtn’ for a mismatch on the reverse strand."

How can I see 'A' at the forward strand, then see 'A' at the reverse strand?

From the result, at position chr21:34124586, it seems it is heterozygous snp A/G. If the gene is expressed on the forward strand. So we should only see A or G on the forward strand. Why it can mapped to the reverse strand. Because only the forward strand DNA has been transcript to mRNA. The reverse strand does not.

I am a bit of confused here. Could any one give me some hits?

Thank you very much in advance.
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