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changes.mady.by.user Deatherage, Daniel E

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Warning
titleMake sure you are on an idev node, or submit as job

The previous command will take quite a bit of time to complete. Therefore you may want to open a new terminal window, and log back into lonestar to do other things while the previous command continues to run.

Code Block
titleCalling variants using samtools and bcftools
cds 
cd BDIB_Human_tutorial
mkdir samtools_example
cd samtools_example
samtools mpileup -uf ../raw_files/ref/hs37d5.fa ../raw_files/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools view -vcg - > trios_tutorial.raw.vcf

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