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, 13:46, 3 December 2014
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| Let's get some information on the BEAGLE VCF: | | Let's get some information on the BEAGLE VCF: |
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− | perl ${GC}/scripts/bed-diff.pl --vcf1 ${SS}/ref22/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/beagle/chr22/chr22.filtered.PASS.beagled.ALL.vcf.gz --out ${OUT}/bedDiff.beagle | + | perl ${GC}/scripts/bed-diff.pl --vcf1 ${SS}/ref22/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/beagle/chr22/chr22.filtered.PASS.beagled.ALL.vcf.gz --out ${OUT}/diffs/bedDiff.beagle |
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| Look at the results: | | Look at the results: |
− | more ${OUT}/bedDiff.beagle.summary | + | more ${OUT}/diffs/bedDiff.beagle.summary |
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| <div class="mw-collapsible mw-collapsed" style="width:400px"> | | <div class="mw-collapsible mw-collapsed" style="width:400px"> |
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| Now, let's see if it improved after running Thunder VCF: | | Now, let's see if it improved after running Thunder VCF: |
− | perl ${GC}/scripts/bed-diff.pl --vcf1 ${SS}/ref22/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --out ${OUT}/bedDiff.thunder | + | perl ${GC}/scripts/bed-diff.pl --vcf1 ${SS}/ref22/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --out ${OUT}/diffs/bedDiff.thunder |
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| Look at the results: | | Look at the results: |
− | more ${OUT}/bedDiff.thunder.summary | + | more ${OUT}/diffs/bedDiff.thunder.summary |
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| <div class="mw-collapsible mw-collapsed" style="width:400px"> | | <div class="mw-collapsible mw-collapsed" style="width:400px"> |