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Old 09-08-2011, 06:42 AM   #1
shuang
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Default How to find out the base on a certain position

I've found a SNP on a certain position on a reference genome (eg chromosome 1, position 13579) by using bwasw and Samtools. Next, I want to find out what is the base on each of my other Sanger sequences. My other Sanger sequences may or may not cover this SNP position.
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Old 09-08-2011, 09:01 AM   #2
volks
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also with samtools mpileup.
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Old 09-08-2011, 09:03 AM   #3
shuang
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Could you tell me more details on how to do it? Maybe give me an example command? Thanks!
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Old 09-08-2011, 09:10 AM   #4
westerman
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Your question is not making sense. Perhaps you can expand on it? As far as I can tell you have (1) found a SNP -- that makes sense -- and (2) want to find out, exactly what?, on your other sequences.
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Old 09-08-2011, 09:15 AM   #5
westerman
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I see that 'volks' responded. I think that he/she is answering the question that you probably meant to ask, which I would state as:

I have found a SNP on a chromosome. I would like to know for all of my sequences what base, if any, they have at that SNP position.

samtools mpileup is the answer for the above. See: http://samtools.sourceforge.net/mpileup.shtml

And, of course, the man page at: http://samtools.sourceforge.net/samtools.shtml

Last edited by westerman; 09-08-2011 at 09:17 AM. Reason: Added man page reference
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Old 09-08-2011, 09:17 AM   #6
shuang
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I want to count the number of each wide-type and polymorphism on the same position among all the sequences which cover that position.
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Old 09-08-2011, 10:18 AM   #7
westerman
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"wide-type"? I'll presume "wild-type".

I was assuming, and perhaps 'volks' was as well, that your Sanger sequences were mapped using bwa and that the information of this mapping is inside your BAM file. If so then 'samtools mpileup your_file' will get you the information you need. You can limit the positions via the '-l' option.
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Old 09-08-2011, 12:17 PM   #8
shuang
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I tried the commands below. I'm sure the sample RN21 has SNP on chr_2:5556282. However, the output showed all the SNPs found in sample RN21. Same as without typing -l chr_2:5,556,282.

What did I miss?


samtools mpileup -uf Sorbil.fasta RN21.ab1.sorted.bam -l chr_2:5,556,282 | /mnt/E_DRIVE/samtools-0.1.17/bcftools/bcftools view -bvcg - > var.raw.bcf


bcftools view var.raw.bcf > var.flt.vcf
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Old 09-09-2011, 05:45 AM   #9
Emilie
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Hi Shuang,

You can use the -r option with a coordinate. You should also write the options before the bam file.
Ex: samtools mpileup -r chr1:38280656-38280656 file.bam

Emilie

****************************************
samtools mpileup [options] in1.bam [in2.bam [...]]
-r STR Only generate pileup in region STR [all sites]
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