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Simply reload samtools using the module system, check the version, and where that version is now being called from.
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execute the following 2 commands and make sure you get the 3rd line as output:
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Follow the same directions to call variants in the BWA or Bowtie2 mapped reads with the improved quality. Just be sure you don't write over your old files. Maybe create new directories like like BDIB_samtools_bwa and and BDIB_samtools_bowtie_improved for the output in each case. You could also try running all of the commands from inside of the samtools_bwa directory, just for a change of pace.
Further Optional Exercises
- 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...
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As another fun version control issue, using the module system you can see that bowtie actually has 2 versions available: 1.1.2 and 2.2.6 ... these version could not be more different to the point where they should really be named different things. bowtie 1.1.2 is included only to keep old scripts that rely on it running, and is surpassed in everyway by bowtie2. If so desired, you could figure out how to run it yourself as a test of learning an unfamiliar program, or you could include any the output from said run from the precanned location below:
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If you do not have the output from the Mapping tutorial, run the first 4 commands to copy over the output that would have been produced. Then, you can immediately start this tutorial! This will be used for the optional bedtools tutorial as well.
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These precanned results will be used in the optional upcoming bedtools tutorial as well, or you can simply compare the output .vcf files for more simple answers |
Further Optional Exercises
- 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?
- Look at how the reads supporting these variants were aligned to the reference genome in the Integrative Genomics Viewer (IGV).
- Look into more sophisticated variant calling with GATK. We recommend starting from the GATK best practice page.
Module version of samtools
As suggested in the initial introduction, the point of this optional tutorial is to work through getting a different version of samtools to work (the command line expectations and flags are not as they were in version 0.1.18). To make sure you are starting in the right place:
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tacc:~$ module load samtools
tacc:~$ which samtools
/opt/apps/samtools/1.3/bin/samtools
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Good luck, and remember if you undertake this and get frustrated with it, it is a great learning experience and is by far the most difficult thing you will attempt. As part of the learning experience, feel free to contact us with any questions or problems you are specifically having with it, but cookbooked suggestions would defeat the intended purpose of beating your head against the problem to figure it out. You DO have the necessary skills to figure out how to do this now.