Question: (Closed) How to do batch processing with mpileup in a Linux shell for loop?
0
gravatar for elvissober
5.0 years ago by
elvissober20
South Africa
elvissober20 wrote:

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  

bash shell samtools • 1.2k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by elvissober20

Hello elvissober!

We believe that this post does not fit the main topic of this site.

Please look up bash loops. Do not open multiple questions addressing the same question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 5.0 years ago by _r_am31k
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