Open info-97 opened 4 years ago
In my testing, survivor adds one to START for some reason, instead of subtracting one. Does this have to do with strand (don't see why though)? Also, it doesn't seem to have ability to deal with confidence intervals (CIPOS, CIEND).
SURVIVOR vcftobed test.vcf 0 -1 out_survivor.bedpe
##fileformat=VCFv4.1
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
chr1 839442 MantaDEL:123157:0:0:0:0:0 CACCTAGACACACACTCCTGGACACACACACCTAGACACACACACCTGGACAAACACA CT 139 PASS END=839499;SVTYPE=DEL;SVLEN=-57;CIGAR=1M1I57D GT:FT:GQ:PL:PR:SR 0/1:PASS:86:189,0,83:1,0:8,5
chr1 1477835 MantaDEL:123205:0:1:0:1:0 AGCTGGGATTACAGGCACGCGCCACCACGCCTGGCTAATGTTGTATTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCTAACTCCCGACCTCAGGTGATCCACCCGCCTCGGCCTCTCAAACT A 27 PASS END=1477968;SVTYPE=DEL;SVLEN=-133;CIGAR=1M133D;CIPOS=0,34;HOMLEN=34;HOMSEQ=GCTGGGATTACAGGCACGCGCCACCACGCCTGGC GT:FT:GQ:PL:PR:SR 0/1:PASS:27:77,0,324:18,0:32,3
chr1 1565630 MantaDUP:TANDEM:123223:0:1:0:0:0 G <DUP:TANDEM> 94 PASS END=1565727;SVTYPE=DUP;SVLEN=97;CIPOS=0,1;CIEND=0,1;HOMLEN=1;HOMSEQ=T GT:FT:GQ:PL:PR:SR 0/1:PASS:94:144,0,772:27,0:53,9
chr1 1595101 MantaDEL:123214:0:0:0:1:0 TGACAGAGAGAGGCAGAGAGAGAGAGAGAGAGACAGACACAGAGAGAGCAGAACAGGGAGAAACAGAGAGACAGAGAGCGAGA T 238 MaxDepth END=1595183;SVTYPE=DEL;SVLEN=-82;CIGAR=1M82D;CIPOS=0,2;HOMLEN=2;HOMSEQ=GA GT:FT:GQ:PL:PR:SR 0/1:PASS:238:288,0,341:10,0:41,10
chr1 839443 839443 chr1 839500 839500 MantaDEL:123157:0:0:0:0:0 , + - DEL
chr1 1477836 1477836 chr1 1477969 1477969 MantaDEL:123205:0:1:0:1:0 , + - DEL
chr1 1565631 1565631 chr1 1565728 1565728 MantaDUP:TANDEM:123223:0:1:0:0:0 , - + DUP
chr1 1595102 1595102 chr1 1595184 1595184 MantaDEL:123214:0:0:0:1:0 , + - DEL
Dear @info-97 sorry for the delay. Dear @ManavalanG thanks for bringing this up again. I have now incorporated the -1 for the positions and included CIPOS and CIEND that wasn't previously used. I report now the start and end breakpoint from the VCF file in the later columns and the start1 + start2 are including CIPOS and the same for END1+2.
Please reclone the code and let me know if that works. Thanks Fritz
Hello fritzsedlazeck,
Thank you for this wonderful tool! I actually noticed that SURVIVOR doesn’t convert VCF to BEDPE start position correctly (i.e start position remains as 1 based rather than 0 based for a BEDPE file...Maybe this is a minor issue to fix but thought worth pointing out.
Thanks!