chr21: subset vs. fullrun

gistfile1.md

chr21 subset lumpy results:

>cat 3_2014-05-06_ceu-sort-svs-NA12878-filter.bedpe | awk '$1=='21' || $4=='21'' | cut -f11 | sort | uniq -c
    212 TYPE:DELETION
     43 TYPE:DUPLICATION
      5 TYPE:INTERCHROM
     10 TYPE:INVERSION

Full CEU lumpy results (chr21):

>cat 2_2014-03-21_ceu-sort-svs-NA12878-filter.bedpe | awk '$1=='21' || $4=='21'' | cut -f11 | sort | uniq -c 
    201 TYPE:DELETION
     55 TYPE:DUPLICATION
    518 TYPE:INTERCHROM
     14 TYPE:INVERSION

Deletions	Count	In Truth Set
Shared	175	33 (18.9%)
Subset Only	37	6 (16.2%)
Fullrun Only	26	1 (3.8%)

chr21 subset lumpy PASS results:

>cat 3_2014-05-06_ceu-sort-svs-NA12878-filter.bedpe | awk '$1=='21' || $4=='21'' | grep PASS | cut -f11 | sort | uniq -c
     85 TYPE:DELETION
     31 TYPE:DUPLICATION
      1 TYPE:INTERCHROM
      5 TYPE:INVERSION

Full CEU lumpy PASS results (chr21):

>cat 2_2014-03-21_ceu-sort-svs-NA12878-filter.bedpe | awk '$1=='21' || $4=='21'' | grep PASS | cut -f11 | sort | uniq -c
     92 TYPE:DELETION
     36 TYPE:DUPLICATION
    245 TYPE:INTERCHROM
      6 TYPE:INVERSION

Deletions	Count	In Truth Set
Shared	76	22 (28.9%)
Subset Only	9	3 (33.3%)
Fullrun Only	16	1 (6.3%)