Off topic:How to do batch processing with mpileup in a Linux shell for loop?
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8.3 years ago
elvissober ▴ 20

I want to make VCFs on a set of .sams (.bams):

for I in ls (*.sam) # calling variants on .sam files
do
    ./samtools mpileup -R -d | bcftools view -g - > test.vcf $i # what to write here correctly?
done
shell bash samtools • 1.6k views
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