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, 10:47, 17 June 2014
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| </div> | | </div> |
| | | |
− | === 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 |
| + | |
| + | <div class="mw-collapsible mw-collapsed" style="width:200px"> |
| + | *Results |
| + | <div class="mw-collapsible-content"> |
| + | 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 |
| + | </div> |
| + | </div> |
| + | |
| + | 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 |
| + | |
| + | <div class="mw-collapsible mw-collapsed" style="width:200px"> |
| + | *Results |
| + | <div class="mw-collapsible-content"> |
| + | 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 |
| + | </div> |
| + | </div> |
| + | |
| + | There is an improvement. |