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Revision as of 13:46, 3 December 2014
, 13:46, 3 December 2014→Improvements
Let's get some information on the BEAGLE VCF:
Let's get some information on the BEAGLE VCF:
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
Look at the results:
Look at the results:
more ${OUT}/bedDiff.beagle.summary
more ${OUT}/diffs/bedDiff.beagle.summary
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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
Look at the results:
Look at the results:
more ${OUT}/bedDiff.thunder.summary
more ${OUT}/diffs/bedDiff.thunder.summary
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