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Revision as of 10:47, 17 June 2014
, 10:47, 17 June 2014→diff
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=== diff ===
=== Improvements ===
perl ${EXT}/bed-diff.pl --vcf1 ${REF}/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --gcRoot ${GC} --out ${OUT}/bedDiff.out
Let's get some information on the BEAGLE VCF:
perl ${EXT}/bed-diff.pl --vcf1 ${REF}/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/beagle/chr22/chr22.filtered.PASS.beagled.ALL.vcf.gz --gcRoot ${GC} --out ${OUT}/bedDiff.beagle
Look at the results:
more ${OUT}/bedDiff.beagle.summary
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*Results
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OVERALL: 43601 44293 0.9844
NREF-EITHER: 19667 20359 0.9660
NMAJ-EITHER: 14585 15277 0.9547
HOMREF: 23934 100 1 0.9958
HET: 329 11959 175 0.9596
HOMALT: 4 83 7708 0.9888
HOMMAJ: 29016 126 2 0.9956
HET: 364 11959 140 0.9596
HOMMIN: 3 57 2626 0.9777
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Now, let's see if it improved after running Thunder VCF:
perl ${EXT}/bed-diff.pl --vcf1 ${REF}/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --gcRoot ${GC} --out ${OUT}/bedDiff.thunder
Look at the results:
more ${OUT}/bedDiff.thunder.summary
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*Results
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OVERALL: 43685 44293 0.9863
NREF-EITHER: 19758 20366 0.9701
NMAJ-EITHER: 14688 15296 0.9603
HOMREF: 23927 106 2 0.9955
HET: 286 12057 120 0.9674
HOMALT: 6 88 7701 0.9879
HOMMAJ: 28997 144 3 0.9950
HET: 286 12057 120 0.9674
HOMMIN: 5 50 2631 0.9795
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There is an improvement.
