MAINTENANCE OUTAGE: The University Wiki Service will undergo maintenance on Thursday March 23rd from 8:00 p.m. until 10:00 p.m.
During this planned maintenance window, wikis.utexas.edu may be unavailable.
Users are advised to save content locally that may be needed during this time and to save all edits before maintenance begins, as unsaved work may be lost.
Bioinformatics Team (BioITeam) at the University of Texas
Space shortcuts
Page tree

Versions Compared

Old Version 5

changes.mady.by.user Geoffrey R Colburn

Saved on

compared with

New Version 6

changes.mady.by.user Geoffrey R Colburn

Saved on

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.