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63 bytes added
, 11:03, 22 May 2015
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| 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 |
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| ==== Annotation / Lookup against dbSNP ==== | | ==== Annotation / Lookup against dbSNP ==== |
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| 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. |
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| 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 |
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