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samtools mpileup -uf samtools_bowtie/REL606.5.fasta samtools_bowtie/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools_bowtie/output.vcf
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Results on Lonestar
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/corral-repl/utexas/BioITeam/ngs_course/mapping/samtools_bowtie/sorted_REL606.5.bam
/corral-repl/utexas/BioITeam/ngs_course/mapping/samtools_bowtie/output.vcf
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/corral-repl/utexas/BioITeam/ngs_course/mapping/samtools_bwa/sorted_REL606.5.bam
/corral-repl/utexas/BioITeam/ngs_course/mapping/samtools_bwa/output.vcf
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Exercise.
VCF format has Allele Frequency tags denoted by AF1. Try the following command to see what value we have in our files.
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