HenrikBengtsson
commented
3 years ago Better late than never. Gains and losses should be presented as DUP and DEL in the ALT field of the exported VCF file when using exportBins(calls, ..., format = "vcf") as in:
library(QDNAseq)
data(LGG150)
data <- LGG150
data <- correctBins(data)
fit <- segmentBins(data)
fit <- callBins(fit)
file <- "LGG150.vcf"
exportBins(fit, format = "vcf", file = file)$ cat LGG150.vcf
##fileformat=VCFv4.2
##source=QDNAseq-1.29.2.9000
##REF=<ID=DIP,Description="CNV call">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##FILTER=<ID=LOWQ,Description="Filtered due to call in low quality region">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of variant: DEL,DUP,INS">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of variant">
##INFO=<ID=BINS,Number=1,Type=Integer,Description="Number of bins in call">
##INFO=<ID=SCORE,Number=1,Type=Integer,Description="Score of calling algorithm">
##INFO=<ID=LOG2CNT,Number=1,Type=Float,Description="Log 2 count">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LGG150
7 1 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=61650000;SVLEN=61650000;BINS=506;SCORE=-1;LOG2CNT=-5.13 GT 0/1
7 61650001 . <DIP> <DUP> 1000 PASS SVTYPE=DUP;END=61980000;SVLEN=330000;BINS=16;SCORE=1;LOG2CNT=1.49 GT 0/1
7 62760001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=102330000;SVLEN=39570000;BINS=2633;SCORE=-1;LOG2CNT=-817.65 GT 0/1
7 140190001 . <DIP> <DUP> 1000 PASS SVTYPE=DUP;END=140235000;SVLEN=45000;BINS=3;SCORE=1;LOG2CNT=4.64 GT 0/1
7 143220001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=153855000;SVLEN=10635000;BINS=77;SCORE=-1;LOG2CNT=-633.38 GT 0/1
8 1 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=7020000;SVLEN=7020000;BINS=468;SCORE=-1;LOG2CNT=-919.72 GT 0/1
8 7020001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=8055000;SVLEN=1035000;BINS=67;SCORE=-2;LOG2CNT=-656.5 GT 1/1
8 11910001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=145500000;SVLEN=133590000;BINS=49;SCORE=-1;LOG2CNT=-634.48 GT 0/1
9 1 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=38835000;SVLEN=38835000;BINS=2589;SCORE=-1;LOG2CNT=-340.76 GT 0/1
9 38835001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=68175000;SVLEN=29340000;BINS=654;SCORE=-2;LOG2CNT=-782.82 GT 1/1
9 68175001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=69015000;SVLEN=840000;BINS=38;SCORE=-1;LOG2CNT=-187.84 GT 0/1
9 69015001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=70980000;SVLEN=1965000;BINS=114;SCORE=-2;LOG2CNT=-708.04 GT 1/1
9 70980001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=141165000;SVLEN=70185000;BINS=4651;SCORE=-1;LOG2CNT=-1.18 GT 0/1
10 60001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=46905000;SVLEN=46845000;BINS=2902;SCORE=-1;LOG2CNT=-1.39 GT 0/1
10 46905001 . <DIP> <DUP> 1000 PASS SVTYPE=DUP;END=47160000;SVLEN=255000;BINS=17;SCORE=1;LOG2CNT=0.41 GT 0/1
10 47160001 . <DIP> <DEL> 1000 PASS SVTYPE=DEL;END=135525000;SVLEN=88365000;BINS=5708;SCORE=-1;LOG2CNT=-806.97 GT 0/1
How could I export a list of calls (gains/losses) obtained from the 'callBins' function into a vcf format?