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Right now, we'll be using it to call variants (find mutations) in the re-sequenced E. coli genome from the Mapping tutorial. You will need the output SAM files from that tutorial to continue here.


If you do not have the output from the Mapping tutorial, run these commands to copy over the output that would have been produced. Then, you can immediately start this tutorial!

Code Block

mkdir intro_to_mapping
cd intro_to_mapping
cp -r $BI/ngs_course/intro_to_mapping/bowtie .
cp -r $BI/ngs_course/intro_to_mapping/bwa . 
cp -r $BI/ngs_course/intro_to_mapping/bowtie2 .

We assume that you are still working in the main directory of called intro_to_mapping data that you copied to created on $SCRATCH.

Load SAMtools

Load the SAMtools module (if not already loaded).


Code Block
mkdir comparison
cp samtools_bowtie/SRR030257.vcf comparison/bowtie.vcf
cp samtools_bwa/SRR030257.vcf comparison/bwa.vcf
cp samtools_bowtie2/SRR030257.vcf comparison/bowtie2.vcf
cd comparison

Use the subcommands bedtools intersect and bedtools subtract we can find equal and different predictions between mappers. Try to figure out how to to do this on your own first. Hint: Remember that adding > output.vcf to the end of a command will pipe the output that is to the terminal into a file, so that you can save it.


  • Which mapper finds more variants?
  • Can you figure out how to filter the VCF files on various criteria, like coverage, quality, ... ?
  • How many high quality mutations are there in these E. coli samples relative to the reference genome?


From here...

Look at how the reads supporting these variants were aligned to the reference genome in the Integrative Genomics Viewer (IGV) tutorial.