Deleted:output as input new function
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4 weeks ago
gubrins ▴ 130

Heys,

I'm working with samtools view to check a specific region from my bam file and I would like to convert that region into fasta piping it to angsd. However, I'm not being able to do it. How should I indicate I want the output as the input? I tried several things but they didn't work:

samtools view -b my.bam chrom | angsd -i -  -doFasta 3 -out my.fasta

Any help would be welcomed!

bash • 160 views
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