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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
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An big inversion reported as BND (lumpyexpress) #217

Open MehmetGoktay opened 6 years ago

MehmetGoktay commented 6 years ago

Hi,

I have been working with couple of accessions which I know they have a big inversion. When I run among those samples, I would expect to see this inversion for all of these accessions. But I could find this inversion for some of the accessions. When I looked in detail, I figured it out that actually it finds this Structural Variation (Inversion) for all but sometimes it outputs as inversions and sometimes outputs as BND.

Is there anything that I can do rather than looking at all bnds to find this inversion?

ryanlayer commented 6 years ago

Interesting, can you paste in an example of each case?

On Thu, Nov 23, 2017 at 3:16 AM, MehmetGoktay notifications@github.com wrote:

Hi,

I have been working with couple of accessions which I know they have a big inversion. When I run among those samples, I would expect to see this inversion for all of these accessions. But I could find this inversion for some of the accessions. When I looked in detail, I figured it out that actually it finds this Structural Variation (Inversion) for all but sometimes it outputs as inversions and sometimes outputs as BND.

Is there anything that I can do rather than looking at all bnds to find this inversion?

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MehmetGoktay commented 6 years ago

NC_003075.7 1612608 3519_1 N N]NC_003075.7:2782621] . . SVTYPE=BND;STRANDS=++:39;EVENT=3519;MATEID=3519_2;CIPOS=-2,1;CIEND=-2,1;CIPOS95=0,0;CIEND95=0,0;SU=39;PE=22;SR=17 GT:SU:PE:SR ./.:39:22:17

NC_003075.7 1612608 3427 N . . SVTYPE=INV;STRANDS=++:46,--:27;SVLEN=1170012;END=2782620;CIPOS=-10,6;CIEND=0,0;CIPOS95=0,0;CIEND95=0,1;IMPRECISE;SU=73;PE=39;SR=34 GT:SU:PE:SR ./.:73:39:34

As you can see this is the inversion that I was looking for but in the first example it just output it as BND rather than INV.