3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 (view source)
Revision as of 12:17, 15 June 2014
, 12:17, 15 June 2014→Filtered VCF
Remember, use <code>'q'</code> to exit out of <code>less</code>
Remember, use <code>'q'</code> to exit out of <code>less</code>
q
q
Now, let's look at the filtered file with genotypes.
less -S ${OUT}/vcfs/chr22/chr22.filtered.vcf.gz
* Scroll down until you find some variants.
** Use space bar to jump a full page
** Use down arrow to move down one line
* Scroll right until you should see per sample genotype information
<div class="mw-collapsible mw-collapsed" style="width:250px">
* View annotated screenshot:
<div class="mw-collapsible-content">
[[File:SvmFiltGL.png|550px]]
</div>
</div>
== GotCloud Genotype Refinement ==
== GotCloud Genotype Refinement ==
${GC}/gotcloud ldrefine --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
${GC}/gotcloud ldrefine --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
