Hi, I am trying to merge with jasmine three VCFs of three different samples, creating a multisample vcf.
I have created two synthetic vcfs containing the following variants:
VCF1 (without header):
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1770S
chr1 100 chr1:100-200 A <DUP> . PASS SVTYPE=<DUP>;END=200;NEXONS=2;BF=4.89;SVLEN=100;RATIO=2.85 GT 0/1
chr1 1000 chr1:1000-1100 A <DEL> . PASS SVTYPE=<DEL>;END=1100;NEXONS=2;BF=10.4;SVLEN=100;RATIO=0.14 GT 0/1
chr1 10000 chr1:[10000-10100](tel:10000-10100) A <DUP> . PASS SVTYPE=<DUP>;END=10100;NEXONS=5;BF=6.68;SVLEN=100;RATIO=1.56 GT 0/1
VCF2 (without header):
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 19N1898
chr1 160 chr1:160-260 C <DUP> . PASS SVTYPE=<DUP>;END=260;NEXONS=4;BF=8.69;SVLEN=100;RATIO=1.93 GT 0/1
chr1 1050 chr1:1050-1150 G <DEL> . PASS SVTYPE=<DEL>;END=1150;NEXONS=9;BF=7.87;SVLEN=100;RATIO=1.37 GT 0/1
chr1 10040 chr1:[10040-10140](tel:10040-10140) C <DUP> . PASS SVTYPE=<DUP>;END=10140;NEXONS=1;BF=5.48;SVLEN=100;RATIO=0.339 GT 0/1
The first variant of each VCF has an overlap of 40%, the second an overlap of 50%, the third an overlap of 60%.
We aim of merging the variants with an overlap of at least 50%.
We obtain the correct result with the following command:
jasmine file_list=filelist.txt out_file=merged_test.vcf min_overlap=1.0 --output_genotypes --default_zero_genotype --leave_breakpoints max_dist_linear=0.5 min_dist=-1
which merges the second variant of VCF1 with the second of VCF2 and the third of VCF1 with the third of VCF2.
Reading the DOC and other issues it seems that the overlap of 50% is used with "min_overlap=0.5" and "max_dist_linear=1.0", but with the following command:
jasmine file_list=filelist.txt out_file=merged_test.vcf min_overlap=1.0 --output_genotypes --default_zero_genotype --leave_breakpoints max_dist_linear=0.5 min_dist=-1
jasmine all three variants of the VCFs.
Hi, I am trying to merge with jasmine three VCFs of three different samples, creating a multisample vcf. I have created two synthetic vcfs containing the following variants:
VCF1 (without header):
VCF2 (without header):
The first variant of each VCF has an overlap of 40%, the second an overlap of 50%, the third an overlap of 60%. We aim of merging the variants with an overlap of at least 50%.
We obtain the correct result with the following command:
jasmine file_list=filelist.txt out_file=merged_test.vcf min_overlap=1.0 --output_genotypes --default_zero_genotype --leave_breakpoints max_dist_linear=0.5 min_dist=-1which merges the second variant of VCF1 with the second of VCF2 and the third of VCF1 with the third of VCF2.Reading the DOC and other issues it seems that the overlap of 50% is used with "min_overlap=0.5" and "max_dist_linear=1.0", but with the following command:
jasmine file_list=filelist.txt out_file=merged_test.vcf min_overlap=1.0 --output_genotypes --default_zero_genotype --leave_breakpoints max_dist_linear=0.5 min_dist=-1jasmine all three variants of the VCFs.