Open main menu

Genome Analysis Wiki β

Changes

diff
</div>
=== Improvements === 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.outthunder 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.