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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
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SV lengths #187

Closed cfz1998 closed 2 years ago

cfz1998 commented 2 years ago

Hi!When i check the smoove result. I find the DUP length is so large! I don't know why! Could somebody HELP me! chr1LG6 13106184 1330202 N <DUP> 23.44 . SVTYPE=DUP;SVLEN=251422240;END=264528424;STRANDS=-+:242;CIPOS=-2,2;CIEND=-2,2;CIPOS95=0,0;CIEND95=0,0;SU=242;PE=0;SR=242;SNAME=JI1539:9601,JI1093:5324,JI1980:3252,JI2348:2994,JI0058:2905,JI0328:7438,JI0015:4584,JI2083:6297,JI1092:5342,JI1794:5544,JI0083:3926,JI1094:5078,JI1088:5669,JI2517:7324,JI1491:5591,JI0132:5445,JI2548:5525,JI2350:5435,JI1585:4140,JI2530:6907,JI1587:3901,JI3511:4328,JI1313:4199,JI3604:3388,JI0932:5457,JI1542:7941,JI1469:5915,JI3148:5486,JI1132:3599,JI3159:5834,JI1626:3375,JI3157:5419,JI1395:3143,JI2115:5358,JI2698:6670,JI3156:5585,JI0554:3308,JI1084:3914,JI0268:3841;ALG=PROD;GCF=0.309327 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB:DHFC:DHFFC:DHBFC 0/1:23:23.44:-4,-2,-4:53:46:6:45:5:28:2:0:17:2:0.1:0.764706:0.8125:0.764706 Thank you very much!

brentp commented 2 years ago

That's a spurious call. That happens sometimes, but this one has low quality, low support and no evidence from duphold annotations (DH*)

cfz1998 commented 2 years ago

Hi,brentp! How should I filter these spurious calls to get high quality SV results? It is very important to me! image In other words, how should I filter the results of the third step, because the results of this step need to be used to merge later. Thanks a lot for your reply!

brentp commented 2 years ago

I would just filter them after the final step.

cfz1998 commented 2 years ago

I would just filter them after the final step.

Thanks a lot! I will try. brentp. --zcf