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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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
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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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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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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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