How to use Samtools to output a list of SNPs (RS number) from a BAM file

[Michael Zhou]

Hi,
I am doing whole exome sequencing. I have a BAM file from 1000 genome website and I want to output its list of SNPs (rs number) and compare with our list of SNPs of this sample from our own sequencing.

1. How can I get the ts list of SNPs (rs number) from this BAM file this using Samtools?

2. Can I compare two BAM files and output the common SNPs (rs number) and differences (ra numbers) from those two BAM files using Samtools?

Please advise!

Michael

[Michael Zhou]

Hi,
I am doing whole exome sequencing. I have a BAM file from 1000 genome website and I want to output its list of SNPs (rs number) and compare with our list of SNPs of this sample from our own sequencing.

1. How can I get the ts list of SNPs (rs number) from this BAM file this using Samtools?

2. Can I compare two BAM files and output the common SNPs (rs number) and differences (ra numbers) from those two BAM files using Samtools?

Please advise!

Michael

[swbarnes2]

samtools mpileup into bcftools is how SAMTools calls SNPs. And you can give it multiple .bams at the same time, if you want.

But samtools is not magic, and does not know of other SNPs. But you can use BEDTools to get the intersect between your SNPs and another file of SNPs with rs IDs.

[CraigJ]

There is a detailed explanation page on the samtools website about calling SNPs with samtools/bcftools, even for multiple samples.

Check out and read the webpage: http://samtools.sourceforge.net/mpileup.shtml

This page plus the samtools manual page should be good to get you started on what you want to do.