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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR didn't merge all SVs into output vcf #163

Open pxchen110 opened 2 years ago

pxchen110 commented 2 years ago

Hi Fritz,

I am trying to merge insertion variants from some vcfs and one of them is generated from DRAGEN.

Here is my SURVIVOR command: SURVIVOR merge input_ins_vcfs 1000 1 1 1 0 0 union6_ins_survivor.vcf (I change the last parameter to 0 for allowing all variants in input vcfs be merged in.)

However, I find that some variants from DRAGEN are not merged in and most of them don't have precise SVLEN information Here is an example of not merged in variant: 1 90370560 MantaINS:23588:0:0:0:3:0 T <INS> 510 PASS END=90370560;SVTYPE=INS;CIPOS=0,6;CIEND=0,6;HOMLEN=6;HOMSEQ=GGAGGT;LEFT_SVINSSEQ=GGAGGTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGAGGGGTTGGGGGTGGTGG;RIGHT_SVINSSEQ=CACCAGTATCCTTGCTTTTATAGTTCATTGCACCGCTTATTTTTTCTTTGCAGGCAAACGAATTTTTACATGGAATTTCTTGTTTTTGGCGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTAGGACTACAGGCGCCCGCCACTACGCCCGGCTATTTTTTGTAGTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTC GT:FT:GQ:PL:PR:SR 0/1:PASS:99:560,0,232:9,6:12,15

How could I change the parameter in order to merge all variants from input vcfs?

Thanks so much, Pinxuan

leonvanmierlo commented 1 year ago

Hi,

I'm not an author but I'm running into the same problem.

Did you find a solution already?

Best regards

MikeWLloyd commented 5 months ago

It does appear to be related to the lack of SVLEN in MantaINS calls. If you spoof a file that includes fake SVLEN values, the MantaINS calls will merge.