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titleClick here for commands and expected output if you are not sure
Code Block
languagebash
titleactivate conda envrionment
conda activate GVA2021
Code Block
languagebash
titleMake sure you have the expected versions of samtools and bcftools installed
samtools --version
bcftools --version


samtools --version output:

No Format
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.

bcftools --version output:

No Format
bcftools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
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titleWhat to do if you do not get version 1.9 for both samtools and bcftools in the above version checks?

The #1 most likely issue here will be that you see samtools version 1.7 rather than 1.9 and will suggest that somewhere in other modifications of the GVA2021 environment, we introduced a change to either samtools or opensssl. If you experience this error, let me know, I'm trying to track down if this is something that a tutorial specifically caused, or if its an error of installing some other tool into this environment mistakenly.

The simplest solution will be to create a new conda environment, and install just samtools, bcftools, and openssl verison 1.0 in it, as we did when we originally installed them into the GVA2021 environment.

Code Block
languagebash
conda create --name GVA-samtools -c bioconda samtools bcftools openssl=1.0
conda activate GVA-samtools

If you need to do this, make sure you are in the new GVA-samtools conda environment before using any of the samtools commands listed here, or switch to it when you get the error message about libcripto



Code Block
languagebash
titleCalling variants using samtools and bcftools. Note the last command is quite long and may wrap around 2 lines your monitor or extend to the right of what you can see without scrolling over
linenumberstrue
mkdir samtools_example
cd samtools_example
samtools mpileup -u -f $SCRATCH/GVA_Human_trios/raw_files/ref/hs37d5.fa $SCRATCH/GVA_Human_trios/raw_files/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools call -v -c - > trios_tutorial.raw.vcf

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