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Revision as of 11:03, 22 May 2015
, 11:03, 22 May 2015→Friday : More SNP Analysis
export HK=/net/seqshop-server/home/hmkang/apigenome/bin
export HK=/net/seqshop-server/home/hmkang/apigenome/bin
export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/
export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/
export REF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref/gotcloud.ref
==== Annotation / Lookup against dbSNP ====
==== Annotation / Lookup against dbSNP ====
Want to see this from the BAM file? Use samtools tview:
Want to see this from the BAM file? Use samtools tview:
$GC/bin/samtools tview $SAMPLE/output/bams/$SAMPLE.recal.bam $GC/gotcloud.ref/human.g1k.v37.fa
$GC/bin/samtools tview $SAMPLE/output/bams/$SAMPLE.recal.bam $REF/hs37d5.fa
Use 'g' & enter the Chr:Pos
Use 'g' & enter the Chr:Pos
* Some patterns may indicate not real variants.
* Some patterns may indicate not real variants.
The phred score at the last column quantifies the degree of functional significance
The phred score at the last column quantifies the degree of functional significance
