I recently tried SVmerge command to merge my SV vcfs. I found that in deletion, SVmerge can't merge variants with DEL tags correctly (even if they all have END INFO ), for example:
variants called from Delly :
14 65360386 DEL00021614 A <DEL> 1800 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.7;END=65363541;PE=18;MAPQ=60;CT=3to5;CIPOS=-12,12;CIEND=-12,12;SRMAPQ=60;INSLEN=0;HOMLEN=11;SR=12;SRQ=0.989247;CONSENSUS=CACTGTTATAAGAGATTTTATTCCTCTTAAAATAAATTCTTATCTAAAACTGTAGGATTGGCCAGAAGTGTTGGCATGAGAAAGAAGGGTTCATTAAAGAATTTTCATAGTGGGAATCTGGATAAAAATCTCCTGTGAAAATAGCAGAGGCCTCCAAAAGAAGGCGTGAAGAGGAAGATGTATGTG;CE=1.90955 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-51.7762,0,-12.3817:99:PASS:202:105:207:1:16:20:7:20
variants called from manta:
14 65360386 MantaDEL:0:25633:25636:0:0:0 A <DEL> 825 PASS END=65363540;SVTYPE=DEL;SVLEN=-3154;CIPOS=0,10;CIEND=0,10;HOMLEN=10;HOMSEQ=AAGAATTTTC GT:FT:GQ:PL:PR:SR 0/1:PASS:99:875,0,330:19,20:18,14
variants called from dragen:
14 65360386 MantaDEL:3966:7:8:0:0:0 A <DEL> 953 PASS END=65363540;SVTYPE=DEL;SVLEN=-3154;CIPOS=0,10;CIEND=0,10;HOMLEN=10;HOMSEQ=AAGAATTTTC GT:FT:GQ:PL:PR:SR 0/1:PASS:99:999,0,359:22,18:17,14
These three variants should be merged by SVmerge, however, they are not merged and output as:
14 65360386 DEL00021614 A <DEL> 1800 PASS ClusterIDs=DEL00021614;NumClusterSVs=1;ExactMatchIDs=DEL00021614;NumExactMatchSVs=1;ClusterMaxShiftDist=NA;ClusterMaxSizeDiff=NA;ClusterMaxEditDist=NA . .
14 65360386 dMantaDEL_3966_7_8_0_0_0 A <DEL> 953 PASS ClusterIDs=dMantaDEL_3966_7_8_0_0_0;NumClusterSVs=1;ExactMatchIDs=dMantaDEL_3966_7_8_0_0_0;NumExactMatchSVs=1;ClusterMaxShiftDist=NA;ClusterMaxSizeDiff=NA;ClusterMaxEditDist=NA . .
14 65360386 mMantaDEL_0_25633_25636_0_0_0 A <DEL> 825 PASS ClusterIDs=mMantaDEL_0_25633_25636_0_0_0;NumClusterSVs=1;ExactMatchIDs=mMantaDEL_0_25633_25636_0_0_0;NumExactMatchSVs=1;ClusterMaxShiftDist=NA;ClusterMaxSizeDiff=NA;ClusterMaxEditDist=NA . .
I would like to ask: How can I merge this kind of variants(without real sequence) correctly by SVmerge? Is there any recommended parameter for this situation ?
Hi nhansen,
I recently tried SVmerge command to merge my SV vcfs. I found that in deletion, SVmerge can't merge variants with DEL tags correctly (even if they all have END INFO ), for example:
variants called from Delly :
14 65360386 DEL00021614 A <DEL> 1800 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.7;END=65363541;PE=18;MAPQ=60;CT=3to5;CIPOS=-12,12;CIEND=-12,12;SRMAPQ=60;INSLEN=0;HOMLEN=11;SR=12;SRQ=0.989247;CONSENSUS=CACTGTTATAAGAGATTTTATTCCTCTTAAAATAAATTCTTATCTAAAACTGTAGGATTGGCCAGAAGTGTTGGCATGAGAAAGAAGGGTTCATTAAAGAATTTTCATAGTGGGAATCTGGATAAAAATCTCCTGTGAAAATAGCAGAGGCCTCCAAAAGAAGGCGTGAAGAGGAAGATGTATGTG;CE=1.90955 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-51.7762,0,-12.3817:99:PASS:202:105:207:1:16:20:7:20variants called from manta:
14 65360386 MantaDEL:0:25633:25636:0:0:0 A <DEL> 825 PASS END=65363540;SVTYPE=DEL;SVLEN=-3154;CIPOS=0,10;CIEND=0,10;HOMLEN=10;HOMSEQ=AAGAATTTTC GT:FT:GQ:PL:PR:SR 0/1:PASS:99:875,0,330:19,20:18,14variants called from dragen:
14 65360386 MantaDEL:3966:7:8:0:0:0 A <DEL> 953 PASS END=65363540;SVTYPE=DEL;SVLEN=-3154;CIPOS=0,10;CIEND=0,10;HOMLEN=10;HOMSEQ=AAGAATTTTC GT:FT:GQ:PL:PR:SR 0/1:PASS:99:999,0,359:22,18:17,14These three variants should be merged by SVmerge, however, they are not merged and output as:
14 65360386 DEL00021614 A <DEL> 1800 PASS ClusterIDs=DEL00021614;NumClusterSVs=1;ExactMatchIDs=DEL00021614;NumExactMatchSVs=1;ClusterMaxShiftDist=NA;ClusterMaxSizeDiff=NA;ClusterMaxEditDist=NA . .14 65360386 dMantaDEL_3966_7_8_0_0_0 A <DEL> 953 PASS ClusterIDs=dMantaDEL_3966_7_8_0_0_0;NumClusterSVs=1;ExactMatchIDs=dMantaDEL_3966_7_8_0_0_0;NumExactMatchSVs=1;ClusterMaxShiftDist=NA;ClusterMaxSizeDiff=NA;ClusterMaxEditDist=NA . .14 65360386 mMantaDEL_0_25633_25636_0_0_0 A <DEL> 825 PASS ClusterIDs=mMantaDEL_0_25633_25636_0_0_0;NumClusterSVs=1;ExactMatchIDs=mMantaDEL_0_25633_25636_0_0_0;NumExactMatchSVs=1;ClusterMaxShiftDist=NA;ClusterMaxSizeDiff=NA;ClusterMaxEditDist=NA . .I would like to ask: How can I merge this kind of variants(without real sequence) correctly by SVmerge? Is there any recommended parameter for this situation ?
Thank you, Pinxuan Chen