Entering edit mode
10 weeks ago
optimistsso4co3 ▴ 100
I called structural variants with MANTA, merged with SURVIVOR for 600 samples. And get thousands of Deletions that basically span the entire chromosome and even have high frequency. There are obviously other variants for these specific individuals for specific chromosome, so i wonder how is that possible?
Here is an example of VCF line for such variant: After manta:
chr1 789563 MantaDEL:22:0:2:1:0:0 **A DEL** 16 MinQUAL END=224012356;SVTYPE=DEL;**SVLEN=-223222793**;IMPRECISE;CIPOS=-74,74;CIEND=-79,79 GT:FT:GQ:PL:PR 0/1:PASS:16:66,0,83:6,4
And after merging with SURVIVOR:
chr1 789563 MantaDEL:24:0:1:0:0:0 **C DEL** 117 PASS SUPP=48;SUPP_VEC=00[....]000;**SVLEN=-223222860**;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=chr1;END=224012378;CIPOS=-77,74;CIEND=-55,1;STRANDS=+- GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/1:NA:223222874:0,0:+-:20:DEL:MantaDEL_33_0_1_0_0_0:NA:NA:chr1_789495-chr1_224012369 [........]
this is quite common , and this is a false positive
Is there a way to remove false positives?