3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for INDELs Practical, December 2014 (view source)
Revision as of 16:00, 17 December 2014
, 16:00, 17 December 2014→Comparison with other data sets
It is usually useful to examine the call sets against known data sets for the passed variants.
It is usually useful to examine the call sets against known data sets for the passed variants.
<div class="mw-collapsible" style="width:500px">
<div class="mw-collapsible mw-collapsed" style="width:500px">
''Command to use at SeqShop Workshop:''
''Command to use at SeqShop Workshop:''
<div class="mw-collapsible-content mw-collapsed">
<div class="mw-collapsible-content">
${GC}/bin/vt profile_indels -g ${SS}/ref22/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
${GC}/bin/vt profile_indels -g ${SS}/ref22/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
</div>
</div>
