no read support or mapping quality info in VCF

[heidihyang]

Hi Fritz,

I've first merged calls from Delly, Lumpy, and Manta for each sample, and then merged all samples into one VCF using SURVIVOR. I tried to run SURVIVOR stats to filter SVs with at least 5 reads supporting them, but when I checked the read support field in the VCF it's empty. MAPQ is also missing. I was wondering if there is a workaround to produce these read support data, or if I should check the outputs from one of these steps? Thanks!

Here's what the INFO part of my VCF looks like:

SUPP=58;SUPP_VEC=1111111111111111111111111111111111111111111111111111111111;SVLEN=-1104;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=CM012293.1;END=19639;CIPOS=0,0;CIEND=0,0;STRANDS=+-
SUPP=58;SUPP_VEC=1111111111111111111111111111111111111111111111111111111111;SVLEN=-15255;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=CM012293.1;END=37823;CIPOS=0,0;CIEND=0,0;STRANDS=+-
SUPP=58;SUPP_VEC=1111111111111111111111111111111111111111111111111111111111;SVLEN=3215;SVTYPE=INV;SVMETHOD=SURVIVOR1.0.7;CHR2=CM012293.1;END=41180;CIPOS=0,168;CIEND=-803,0;STRANDS=--
SUPP=58;SUPP_VEC=1111111111111111111111111111111111111111111111111111111111;SVLEN=1121;SVTYPE=INV;SVMETHOD=SURVIVOR1.0.7;CHR2=CM012293.1;END=40099;CIPOS=-382,0;CIEND=-452,2;STRANDS=++

Best,
Heidi