# BED files # region: chr1 0 500 #input/annoGrator/insertionsPrimary.bed.chrom input/annoGrator/insertionsPrimary.bed.chromStart input/annoGrator/insertionsPrimary.bed.chromEnd input/annoGrator/insertionsPrimary.bed.name input/annoGrator/insertionsSecondary.bed.chrom input/annoGrator/insertionsSecondary.bed.chromStart input/annoGrator/insertionsSecondary.bed.chromEnd input/annoGrator/insertionsSecondary.bed.name chr1 20 20 pil chr1 19 20 jBPil chr1 150 250 pl chr1 150 200 justBefore chr1 150 250 pl chr1 200 200 insLeft chr1 150 250 pl chr1 220 230 inThere chr1 200 300 p chr1 200 200 insLeft chr1 200 300 p chr1 220 230 inThere chr1 200 300 p chr1 300 300 insRight chr1 250 350 pr chr1 300 300 insRight chr1 250 350 pr chr1 300 320 justAfter chr1 400 400 pi chr1 380 400 jBInsPi chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 400 400 insPi chr1 400 400 pi chr1 400 420 jAInsPi # region: chr1 100 200 #input/annoGrator/insertionsPrimary.bed.chrom input/annoGrator/insertionsPrimary.bed.chromStart input/annoGrator/insertionsPrimary.bed.chromEnd input/annoGrator/insertionsPrimary.bed.name input/annoGrator/insertionsSecondary.bed.chrom input/annoGrator/insertionsSecondary.bed.chromStart input/annoGrator/insertionsSecondary.bed.chromEnd input/annoGrator/insertionsSecondary.bed.name chr1 150 250 pl chr1 150 200 justBefore chr1 150 250 pl chr1 200 200 insLeft # region: chr1 200 300 #input/annoGrator/insertionsPrimary.bed.chrom input/annoGrator/insertionsPrimary.bed.chromStart input/annoGrator/insertionsPrimary.bed.chromEnd input/annoGrator/insertionsPrimary.bed.name input/annoGrator/insertionsSecondary.bed.chrom input/annoGrator/insertionsSecondary.bed.chromStart input/annoGrator/insertionsSecondary.bed.chromEnd input/annoGrator/insertionsSecondary.bed.name chr1 150 250 pl chr1 200 200 insLeft chr1 150 250 pl chr1 220 230 inThere chr1 200 300 p chr1 200 200 insLeft chr1 200 300 p chr1 220 230 inThere chr1 200 300 p chr1 300 300 insRight chr1 250 350 pr chr1 300 300 insRight # region: chr1 300 400 #input/annoGrator/insertionsPrimary.bed.chrom input/annoGrator/insertionsPrimary.bed.chromStart input/annoGrator/insertionsPrimary.bed.chromEnd input/annoGrator/insertionsPrimary.bed.name input/annoGrator/insertionsSecondary.bed.chrom input/annoGrator/insertionsSecondary.bed.chromStart input/annoGrator/insertionsSecondary.bed.chromEnd input/annoGrator/insertionsSecondary.bed.name chr1 250 350 pr chr1 300 300 insRight chr1 250 350 pr chr1 300 320 justAfter chr1 400 400 pi chr1 380 400 jBInsPi chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 400 400 insPi # region: chr1 400 500 #input/annoGrator/insertionsPrimary.bed.chrom input/annoGrator/insertionsPrimary.bed.chromStart input/annoGrator/insertionsPrimary.bed.chromEnd input/annoGrator/insertionsPrimary.bed.name input/annoGrator/insertionsSecondary.bed.chrom input/annoGrator/insertionsSecondary.bed.chromStart input/annoGrator/insertionsSecondary.bed.chromEnd input/annoGrator/insertionsSecondary.bed.name chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 400 400 insPi chr1 400 400 pi chr1 400 420 jAInsPi # BigBed files # region: chr1 0 500 #input/annoGrator/insertionsPrimary.bb.chrom input/annoGrator/insertionsPrimary.bb.chromStart input/annoGrator/insertionsPrimary.bb.chromEnd input/annoGrator/insertionsPrimary.bb.name input/annoGrator/insertionsSecondary.bb.chrom input/annoGrator/insertionsSecondary.bb.chromStart input/annoGrator/insertionsSecondary.bb.chromEnd input/annoGrator/insertionsSecondary.bb.name chr1 20 20 pil chr1 19 20 jBPil chr1 150 250 pl chr1 150 200 justBefore chr1 150 250 pl chr1 200 200 insLeft chr1 150 250 pl chr1 220 230 inThere chr1 200 300 p chr1 200 200 insLeft chr1 200 300 p chr1 220 230 inThere chr1 200 300 p chr1 300 300 insRight chr1 250 350 pr chr1 300 300 insRight chr1 250 350 pr chr1 300 320 justAfter chr1 400 400 pi chr1 380 400 jBInsPi chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 400 400 insPi chr1 400 400 pi chr1 400 420 jAInsPi # region: chr1 100 200 #input/annoGrator/insertionsPrimary.bb.chrom input/annoGrator/insertionsPrimary.bb.chromStart input/annoGrator/insertionsPrimary.bb.chromEnd input/annoGrator/insertionsPrimary.bb.name input/annoGrator/insertionsSecondary.bb.chrom input/annoGrator/insertionsSecondary.bb.chromStart input/annoGrator/insertionsSecondary.bb.chromEnd input/annoGrator/insertionsSecondary.bb.name chr1 150 250 pl chr1 150 200 justBefore chr1 150 250 pl chr1 200 200 insLeft # region: chr1 200 300 #input/annoGrator/insertionsPrimary.bb.chrom input/annoGrator/insertionsPrimary.bb.chromStart input/annoGrator/insertionsPrimary.bb.chromEnd input/annoGrator/insertionsPrimary.bb.name input/annoGrator/insertionsSecondary.bb.chrom input/annoGrator/insertionsSecondary.bb.chromStart input/annoGrator/insertionsSecondary.bb.chromEnd input/annoGrator/insertionsSecondary.bb.name chr1 150 250 pl chr1 200 200 insLeft chr1 150 250 pl chr1 220 230 inThere chr1 200 300 p chr1 200 200 insLeft chr1 200 300 p chr1 220 230 inThere chr1 200 300 p chr1 300 300 insRight chr1 250 350 pr chr1 300 300 insRight # region: chr1 300 400 #input/annoGrator/insertionsPrimary.bb.chrom input/annoGrator/insertionsPrimary.bb.chromStart input/annoGrator/insertionsPrimary.bb.chromEnd input/annoGrator/insertionsPrimary.bb.name input/annoGrator/insertionsSecondary.bb.chrom input/annoGrator/insertionsSecondary.bb.chromStart input/annoGrator/insertionsSecondary.bb.chromEnd input/annoGrator/insertionsSecondary.bb.name chr1 250 350 pr chr1 300 300 insRight chr1 250 350 pr chr1 300 320 justAfter chr1 400 400 pi chr1 380 400 jBInsPi chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 400 400 insPi # region: chr1 400 500 #input/annoGrator/insertionsPrimary.bb.chrom input/annoGrator/insertionsPrimary.bb.chromStart input/annoGrator/insertionsPrimary.bb.chromEnd input/annoGrator/insertionsPrimary.bb.name input/annoGrator/insertionsSecondary.bb.chrom input/annoGrator/insertionsSecondary.bb.chromStart input/annoGrator/insertionsSecondary.bb.chromEnd input/annoGrator/insertionsSecondary.bb.name chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 400 400 insPi chr1 400 400 pi chr1 400 420 jAInsPi # BED tables # region: chr1 0 500 #test.insertionsPrimary.chrom test.insertionsPrimary.chromStart test.insertionsPrimary.chromEnd test.insertionsPrimary.name test.insertionsSecondary.chrom test.insertionsSecondary.chromStart test.insertionsSecondary.chromEnd test.insertionsSecondary.name chr1 20 20 pil chr1 19 20 jBPil chr1 150 250 pl chr1 150 200 justBefore chr1 150 250 pl chr1 200 200 insLeft chr1 150 250 pl chr1 220 230 inThere chr1 200 300 p chr1 200 200 insLeft chr1 200 300 p chr1 220 230 inThere chr1 200 300 p chr1 300 300 insRight chr1 250 350 pr chr1 300 320 justAfter chr1 250 350 pr chr1 300 300 insRight chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 380 400 jBInsPi chr1 400 400 pi chr1 400 420 jAInsPi chr1 400 400 pi chr1 400 400 insPi # region: chr1 100 200 #test.insertionsPrimary.chrom test.insertionsPrimary.chromStart test.insertionsPrimary.chromEnd test.insertionsPrimary.name test.insertionsSecondary.chrom test.insertionsSecondary.chromStart test.insertionsSecondary.chromEnd test.insertionsSecondary.name chr1 150 250 pl chr1 150 200 justBefore chr1 150 250 pl chr1 200 200 insLeft # region: chr1 200 300 #test.insertionsPrimary.chrom test.insertionsPrimary.chromStart test.insertionsPrimary.chromEnd test.insertionsPrimary.name test.insertionsSecondary.chrom test.insertionsSecondary.chromStart test.insertionsSecondary.chromEnd test.insertionsSecondary.name chr1 150 250 pl chr1 200 200 insLeft chr1 150 250 pl chr1 220 230 inThere chr1 200 300 p chr1 200 200 insLeft chr1 200 300 p chr1 220 230 inThere chr1 200 300 p chr1 300 300 insRight chr1 250 350 pr chr1 300 300 insRight # region: chr1 300 400 #test.insertionsPrimary.chrom test.insertionsPrimary.chromStart test.insertionsPrimary.chromEnd test.insertionsPrimary.name test.insertionsSecondary.chrom test.insertionsSecondary.chromStart test.insertionsSecondary.chromEnd test.insertionsSecondary.name chr1 250 350 pr chr1 300 320 justAfter chr1 250 350 pr chr1 300 300 insRight chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 380 400 jBInsPi chr1 400 400 pi chr1 400 400 insPi # region: chr1 400 500 #test.insertionsPrimary.chrom test.insertionsPrimary.chromStart test.insertionsPrimary.chromEnd test.insertionsPrimary.name test.insertionsSecondary.chrom test.insertionsSecondary.chromStart test.insertionsSecondary.chromEnd test.insertionsSecondary.name chr1 400 400 pi chr1 380 420 aroundPi chr1 400 400 pi chr1 400 420 jAInsPi chr1 400 400 pi chr1 400 400 insPi # VCF files (uncompressed) # region: chr1 0 500 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.chrom input/annoGrator/insertionsPrimary.vcf.pos input/annoGrator/insertionsPrimary.vcf.id input/annoGrator/insertionsPrimary.vcf.ref input/annoGrator/insertionsPrimary.vcf.alt input/annoGrator/insertionsPrimary.vcf.qual input/annoGrator/insertionsPrimary.vcf.filter input/annoGrator/insertionsPrimary.vcf.info input/annoGrator/insertionsPrimary.vcf.format input/annoGrator/insertionsPrimary.vcf.genotypes input/annoGrator/insertionsSecondary.vcf.chrom input/annoGrator/insertionsSecondary.vcf.pos input/annoGrator/insertionsSecondary.vcf.id input/annoGrator/insertionsSecondary.vcf.ref input/annoGrator/insertionsSecondary.vcf.alt input/annoGrator/insertionsSecondary.vcf.qual input/annoGrator/insertionsSecondary.vcf.filter input/annoGrator/insertionsSecondary.vcf.info input/annoGrator/insertionsSecondary.vcf.format input/annoGrator/insertionsSecondary.vcf.genotypes chr1 20 pil N NA 1 PASS . chr1 20 jBPil N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 150 justBefore 1 PASS END=200 chr1 150 pl 1 PASS END=250 chr1 196 jBS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 jBS1 N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 insLeft N NA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 201 leftS1 N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 220 inThere 1 PASS END=230 chr1 200 p 1 PASS END=300 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 200 p 1 PASS END=300 chr1 200 insLeft N NA 1 PASS . chr1 200 p 1 PASS END=300 chr1 201 leftS1 N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 220 inThere 1 PASS END=230 chr1 200 p 1 PASS END=300 chr1 300 rightS1a N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 rightS1b N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 insRight N NA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS1a N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS1b N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 insRight N NA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 justAfter 1 PASS END=320 chr1 250 pr 1 PASS END=350 chr1 301 jAS1 N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 301 jAS5 NNNNN AAAAA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 380 jBInsPi 1 PASS END=400 chr1 400 pi N NA 1 PASS . chr1 380 aroundPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 396 leftPiS5 NNNNN AAAAA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 leftPiS1 N A 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 aroundPiS2 NN AA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 insPi N NA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 jAInsPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 401 rightPiS1 N A 1 PASS . chr1 400 pi N NA 1 PASS . chr1 401 rightPiS5 NNNNN AAAAA 1 PASS . # region: chr1 100 200 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.chrom input/annoGrator/insertionsPrimary.vcf.pos input/annoGrator/insertionsPrimary.vcf.id input/annoGrator/insertionsPrimary.vcf.ref input/annoGrator/insertionsPrimary.vcf.alt input/annoGrator/insertionsPrimary.vcf.qual input/annoGrator/insertionsPrimary.vcf.filter input/annoGrator/insertionsPrimary.vcf.info input/annoGrator/insertionsPrimary.vcf.format input/annoGrator/insertionsPrimary.vcf.genotypes input/annoGrator/insertionsSecondary.vcf.chrom input/annoGrator/insertionsSecondary.vcf.pos input/annoGrator/insertionsSecondary.vcf.id input/annoGrator/insertionsSecondary.vcf.ref input/annoGrator/insertionsSecondary.vcf.alt input/annoGrator/insertionsSecondary.vcf.qual input/annoGrator/insertionsSecondary.vcf.filter input/annoGrator/insertionsSecondary.vcf.info input/annoGrator/insertionsSecondary.vcf.format input/annoGrator/insertionsSecondary.vcf.genotypes chr1 150 pl 1 PASS END=250 chr1 150 justBefore 1 PASS END=200 chr1 150 pl 1 PASS END=250 chr1 196 jBS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 jBS1 N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 insLeft N NA 1 PASS . # region: chr1 200 300 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.chrom input/annoGrator/insertionsPrimary.vcf.pos input/annoGrator/insertionsPrimary.vcf.id input/annoGrator/insertionsPrimary.vcf.ref input/annoGrator/insertionsPrimary.vcf.alt input/annoGrator/insertionsPrimary.vcf.qual input/annoGrator/insertionsPrimary.vcf.filter input/annoGrator/insertionsPrimary.vcf.info input/annoGrator/insertionsPrimary.vcf.format input/annoGrator/insertionsPrimary.vcf.genotypes input/annoGrator/insertionsSecondary.vcf.chrom input/annoGrator/insertionsSecondary.vcf.pos input/annoGrator/insertionsSecondary.vcf.id input/annoGrator/insertionsSecondary.vcf.ref input/annoGrator/insertionsSecondary.vcf.alt input/annoGrator/insertionsSecondary.vcf.qual input/annoGrator/insertionsSecondary.vcf.filter input/annoGrator/insertionsSecondary.vcf.info input/annoGrator/insertionsSecondary.vcf.format input/annoGrator/insertionsSecondary.vcf.genotypes chr1 150 pl 1 PASS END=250 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 insLeft N NA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 201 leftS1 N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 220 inThere 1 PASS END=230 chr1 200 p 1 PASS END=300 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 200 p 1 PASS END=300 chr1 200 insLeft N NA 1 PASS . chr1 200 p 1 PASS END=300 chr1 201 leftS1 N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 220 inThere 1 PASS END=230 chr1 200 p 1 PASS END=300 chr1 300 rightS1a N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 rightS1b N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 insRight N NA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS1a N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS1b N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 insRight N NA 1 PASS . # region: chr1 300 400 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.chrom input/annoGrator/insertionsPrimary.vcf.pos input/annoGrator/insertionsPrimary.vcf.id input/annoGrator/insertionsPrimary.vcf.ref input/annoGrator/insertionsPrimary.vcf.alt input/annoGrator/insertionsPrimary.vcf.qual input/annoGrator/insertionsPrimary.vcf.filter input/annoGrator/insertionsPrimary.vcf.info input/annoGrator/insertionsPrimary.vcf.format input/annoGrator/insertionsPrimary.vcf.genotypes input/annoGrator/insertionsSecondary.vcf.chrom input/annoGrator/insertionsSecondary.vcf.pos input/annoGrator/insertionsSecondary.vcf.id input/annoGrator/insertionsSecondary.vcf.ref input/annoGrator/insertionsSecondary.vcf.alt input/annoGrator/insertionsSecondary.vcf.qual input/annoGrator/insertionsSecondary.vcf.filter input/annoGrator/insertionsSecondary.vcf.info input/annoGrator/insertionsSecondary.vcf.format input/annoGrator/insertionsSecondary.vcf.genotypes chr1 250 pr 1 PASS END=350 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 insRight N NA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 justAfter 1 PASS END=320 chr1 250 pr 1 PASS END=350 chr1 301 jAS1 N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 301 jAS5 NNNNN AAAAA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 380 jBInsPi 1 PASS END=400 chr1 400 pi N NA 1 PASS . chr1 380 aroundPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 396 leftPiS5 NNNNN AAAAA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 leftPiS1 N A 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 aroundPiS2 NN AA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 insPi N NA 1 PASS . # region: chr1 400 500 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.chrom input/annoGrator/insertionsPrimary.vcf.pos input/annoGrator/insertionsPrimary.vcf.id input/annoGrator/insertionsPrimary.vcf.ref input/annoGrator/insertionsPrimary.vcf.alt input/annoGrator/insertionsPrimary.vcf.qual input/annoGrator/insertionsPrimary.vcf.filter input/annoGrator/insertionsPrimary.vcf.info input/annoGrator/insertionsPrimary.vcf.format input/annoGrator/insertionsPrimary.vcf.genotypes input/annoGrator/insertionsSecondary.vcf.chrom input/annoGrator/insertionsSecondary.vcf.pos input/annoGrator/insertionsSecondary.vcf.id input/annoGrator/insertionsSecondary.vcf.ref input/annoGrator/insertionsSecondary.vcf.alt input/annoGrator/insertionsSecondary.vcf.qual input/annoGrator/insertionsSecondary.vcf.filter input/annoGrator/insertionsSecondary.vcf.info input/annoGrator/insertionsSecondary.vcf.format input/annoGrator/insertionsSecondary.vcf.genotypes chr1 400 pi N NA 1 PASS . chr1 380 aroundPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 400 aroundPiS2 NN AA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 insPi N NA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 jAInsPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 401 rightPiS1 N A 1 PASS . chr1 400 pi N NA 1 PASS . chr1 401 rightPiS5 NNNNN AAAAA 1 PASS . # VCF files (tabix) # region: chr1 0 500 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.gz.chrom input/annoGrator/insertionsPrimary.vcf.gz.pos input/annoGrator/insertionsPrimary.vcf.gz.id input/annoGrator/insertionsPrimary.vcf.gz.ref input/annoGrator/insertionsPrimary.vcf.gz.alt input/annoGrator/insertionsPrimary.vcf.gz.qual input/annoGrator/insertionsPrimary.vcf.gz.filter input/annoGrator/insertionsPrimary.vcf.gz.info input/annoGrator/insertionsPrimary.vcf.gz.format input/annoGrator/insertionsPrimary.vcf.gz.genotypes input/annoGrator/insertionsSecondary.vcf.gz.chrom input/annoGrator/insertionsSecondary.vcf.gz.pos input/annoGrator/insertionsSecondary.vcf.gz.id input/annoGrator/insertionsSecondary.vcf.gz.ref input/annoGrator/insertionsSecondary.vcf.gz.alt input/annoGrator/insertionsSecondary.vcf.gz.qual input/annoGrator/insertionsSecondary.vcf.gz.filter input/annoGrator/insertionsSecondary.vcf.gz.info input/annoGrator/insertionsSecondary.vcf.gz.format input/annoGrator/insertionsSecondary.vcf.gz.genotypes chr1 20 pil N NA 1 PASS . chr1 20 jBPil N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 150 justBefore 1 PASS END=200 chr1 150 pl 1 PASS END=250 chr1 196 jBS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 jBS1 N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 insLeft N NA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 201 leftS1 N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 220 inThere 1 PASS END=230 chr1 200 p 1 PASS END=300 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 200 p 1 PASS END=300 chr1 200 insLeft N NA 1 PASS . chr1 200 p 1 PASS END=300 chr1 201 leftS1 N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 220 inThere 1 PASS END=230 chr1 200 p 1 PASS END=300 chr1 300 rightS1a N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 rightS1b N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 insRight N NA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS1a N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS1b N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 insRight N NA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 justAfter 1 PASS END=320 chr1 250 pr 1 PASS END=350 chr1 301 jAS1 N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 301 jAS5 NNNNN AAAAA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 380 jBInsPi 1 PASS END=400 chr1 400 pi N NA 1 PASS . chr1 380 aroundPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 396 leftPiS5 NNNNN AAAAA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 leftPiS1 N A 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 aroundPiS2 NN AA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 insPi N NA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 jAInsPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 401 rightPiS1 N A 1 PASS . chr1 400 pi N NA 1 PASS . chr1 401 rightPiS5 NNNNN AAAAA 1 PASS . # region: chr1 100 200 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.gz.chrom input/annoGrator/insertionsPrimary.vcf.gz.pos input/annoGrator/insertionsPrimary.vcf.gz.id input/annoGrator/insertionsPrimary.vcf.gz.ref input/annoGrator/insertionsPrimary.vcf.gz.alt input/annoGrator/insertionsPrimary.vcf.gz.qual input/annoGrator/insertionsPrimary.vcf.gz.filter input/annoGrator/insertionsPrimary.vcf.gz.info input/annoGrator/insertionsPrimary.vcf.gz.format input/annoGrator/insertionsPrimary.vcf.gz.genotypes input/annoGrator/insertionsSecondary.vcf.gz.chrom input/annoGrator/insertionsSecondary.vcf.gz.pos input/annoGrator/insertionsSecondary.vcf.gz.id input/annoGrator/insertionsSecondary.vcf.gz.ref input/annoGrator/insertionsSecondary.vcf.gz.alt input/annoGrator/insertionsSecondary.vcf.gz.qual input/annoGrator/insertionsSecondary.vcf.gz.filter input/annoGrator/insertionsSecondary.vcf.gz.info input/annoGrator/insertionsSecondary.vcf.gz.format input/annoGrator/insertionsSecondary.vcf.gz.genotypes chr1 150 pl 1 PASS END=250 chr1 150 justBefore 1 PASS END=200 chr1 150 pl 1 PASS END=250 chr1 196 jBS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 jBS1 N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 insLeft N NA 1 PASS . # region: chr1 200 300 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.gz.chrom input/annoGrator/insertionsPrimary.vcf.gz.pos input/annoGrator/insertionsPrimary.vcf.gz.id input/annoGrator/insertionsPrimary.vcf.gz.ref input/annoGrator/insertionsPrimary.vcf.gz.alt input/annoGrator/insertionsPrimary.vcf.gz.qual input/annoGrator/insertionsPrimary.vcf.gz.filter input/annoGrator/insertionsPrimary.vcf.gz.info input/annoGrator/insertionsPrimary.vcf.gz.format input/annoGrator/insertionsPrimary.vcf.gz.genotypes input/annoGrator/insertionsSecondary.vcf.gz.chrom input/annoGrator/insertionsSecondary.vcf.gz.pos input/annoGrator/insertionsSecondary.vcf.gz.id input/annoGrator/insertionsSecondary.vcf.gz.ref input/annoGrator/insertionsSecondary.vcf.gz.alt input/annoGrator/insertionsSecondary.vcf.gz.qual input/annoGrator/insertionsSecondary.vcf.gz.filter input/annoGrator/insertionsSecondary.vcf.gz.info input/annoGrator/insertionsSecondary.vcf.gz.format input/annoGrator/insertionsSecondary.vcf.gz.genotypes chr1 150 pl 1 PASS END=250 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 200 insLeft N NA 1 PASS . chr1 150 pl 1 PASS END=250 chr1 201 leftS1 N A 1 PASS . chr1 150 pl 1 PASS END=250 chr1 220 inThere 1 PASS END=230 chr1 200 p 1 PASS END=300 chr1 197 leftS5 NNNNN AAAAA 1 PASS . chr1 200 p 1 PASS END=300 chr1 200 insLeft N NA 1 PASS . chr1 200 p 1 PASS END=300 chr1 201 leftS1 N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 220 inThere 1 PASS END=230 chr1 200 p 1 PASS END=300 chr1 300 rightS1a N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 rightS1b N A 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 200 p 1 PASS END=300 chr1 300 insRight N NA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS1a N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS1b N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 insRight N NA 1 PASS . # region: chr1 300 400 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.gz.chrom input/annoGrator/insertionsPrimary.vcf.gz.pos input/annoGrator/insertionsPrimary.vcf.gz.id input/annoGrator/insertionsPrimary.vcf.gz.ref input/annoGrator/insertionsPrimary.vcf.gz.alt input/annoGrator/insertionsPrimary.vcf.gz.qual input/annoGrator/insertionsPrimary.vcf.gz.filter input/annoGrator/insertionsPrimary.vcf.gz.info input/annoGrator/insertionsPrimary.vcf.gz.format input/annoGrator/insertionsPrimary.vcf.gz.genotypes input/annoGrator/insertionsSecondary.vcf.gz.chrom input/annoGrator/insertionsSecondary.vcf.gz.pos input/annoGrator/insertionsSecondary.vcf.gz.id input/annoGrator/insertionsSecondary.vcf.gz.ref input/annoGrator/insertionsSecondary.vcf.gz.alt input/annoGrator/insertionsSecondary.vcf.gz.qual input/annoGrator/insertionsSecondary.vcf.gz.filter input/annoGrator/insertionsSecondary.vcf.gz.info input/annoGrator/insertionsSecondary.vcf.gz.format input/annoGrator/insertionsSecondary.vcf.gz.genotypes chr1 250 pr 1 PASS END=350 chr1 300 rightS5 NNNNN AAAAA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 insRight N NA 1 PASS . chr1 250 pr 1 PASS END=350 chr1 300 justAfter 1 PASS END=320 chr1 250 pr 1 PASS END=350 chr1 301 jAS1 N A 1 PASS . chr1 250 pr 1 PASS END=350 chr1 301 jAS5 NNNNN AAAAA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 380 jBInsPi 1 PASS END=400 chr1 400 pi N NA 1 PASS . chr1 380 aroundPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 396 leftPiS5 NNNNN AAAAA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 leftPiS1 N A 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 aroundPiS2 NN AA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 insPi N NA 1 PASS . # region: chr1 400 500 # Header from primary input: ##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO #input/annoGrator/insertionsPrimary.vcf.gz.chrom input/annoGrator/insertionsPrimary.vcf.gz.pos input/annoGrator/insertionsPrimary.vcf.gz.id input/annoGrator/insertionsPrimary.vcf.gz.ref input/annoGrator/insertionsPrimary.vcf.gz.alt input/annoGrator/insertionsPrimary.vcf.gz.qual input/annoGrator/insertionsPrimary.vcf.gz.filter input/annoGrator/insertionsPrimary.vcf.gz.info input/annoGrator/insertionsPrimary.vcf.gz.format input/annoGrator/insertionsPrimary.vcf.gz.genotypes input/annoGrator/insertionsSecondary.vcf.gz.chrom input/annoGrator/insertionsSecondary.vcf.gz.pos input/annoGrator/insertionsSecondary.vcf.gz.id input/annoGrator/insertionsSecondary.vcf.gz.ref input/annoGrator/insertionsSecondary.vcf.gz.alt input/annoGrator/insertionsSecondary.vcf.gz.qual input/annoGrator/insertionsSecondary.vcf.gz.filter input/annoGrator/insertionsSecondary.vcf.gz.info input/annoGrator/insertionsSecondary.vcf.gz.format input/annoGrator/insertionsSecondary.vcf.gz.genotypes chr1 400 pi N NA 1 PASS . chr1 380 aroundPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 400 aroundPiS2 NN AA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 insPi N NA 1 PASS . chr1 400 pi N NA 1 PASS . chr1 400 jAInsPi 1 PASS END=420 chr1 400 pi N NA 1 PASS . chr1 401 rightPiS1 N A 1 PASS . chr1 400 pi N NA 1 PASS . chr1 401 rightPiS5 NNNNN AAAAA 1 PASS .