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

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  

samtools bash shell • 1.3k views
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