Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Code Block
1bcftools view -vcg - > 03_Output/variant_calling/samtools/output.vcf
titlesamtools mpileup -uf 03_Output/variant_calling/samtools/REL606.5.fasta 03_Output/variant_calling/samtools/REL606.5.bam
borderStylesolid
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bcfview] 100000 sites processed.
[afs] 0:99910.349 1:52.764 2:36.886
[bcfview] 200000 sites processed.
[afs] 0:99946.543 1:48.457 2:5.000
[bcfview] 300000 sites processed.
[afs] 0:99976.591 1:5.410 2:17.999
[bcfview] 400000 sites processed.
[afs] 0:99984.243 1:8.357 2:7.399
[bcfview] 500000 sites processed.
[afs] 0:99970.803 1:23.197 2:6.000
[afs] 0:63952.773 1:6.227 2:2.000

Produces output.vcf.