Changes

From Genome Analysis Wiki
Jump to navigationJump to search

SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 (view source)

Revision as of 16:24, 15 June 2014

267 bytes added ,  16:24, 15 June 2014
→‎Genotype Refinement Output
Line 323: Line 323:  
Use tabix to extract that from the VCFs:
 
Use tabix to extract that from the VCFs:
 
  ${GC}/bin/tabix ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz 22:36907000-36907100 |less -S
 
  ${GC}/bin/tabix ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz 22:36907000-36907100 |less -S
 +
 +
Remember, type 'q' to quit less.
 +
q
    
;Are there any variants in this region?
 
;Are there any variants in this region?
Line 345: Line 348:  
  zcat ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz |grep "#CHROM"
 
  zcat ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz |grep "#CHROM"
 
* That will help you figure out it's genotype.
 
* That will help you figure out it's genotype.
 +
* Rerun the tabix command and scroll to find HG00551's genotype:
 +
${GC}/bin/tabix ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz 22:36907000-36907100 |less -S
 +
 
<ul>
 
<ul>
 
<div class="mw-collapsible mw-collapsed" style="width:500px">
 
<div class="mw-collapsible mw-collapsed" style="width:500px">
Line 357: Line 363:  
</div>
 
</div>
 
</ul>
 
</ul>
 +
 +
Remember, type 'q' to quit less.
 +
q
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/10709"

Navigation menu