Thank you for providing this excellent tool ! Love it so much!
I'm currently using Jasmine to evaluate the presence/absence of SV identified with different SV callers in a small WGS cohort.
Ultimately, I would like to obtain a single non redundant SV VCF with all the samples of my cohort:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3
.
I'm using Jasmine in 2 steps:
Step 1
For each sample of my cohort :
I merge the SVs called with different SV callers (the idea is to determine all SV in a sample, considering all SV type, but without redundancy due to fuzzy coordinates) in order to obtain a unique VCF file for each sample.
sample1_SV_smoove.vcf
sample1_SV_delly.vcf
sample1_SV_CNVpytor.vcf
sample1_SV_Manta.vcf
sample1_SV_Mobster.vcf
sample1_SV_ExpansionHunter.vcf
=========Jasmine======> sample1_SV_merge.vcf
Wanted SV clustering criteria:
=> e.g. a maximum of 300bp distance between breakpoints and at least 80% reciprocal overlap by size.
I don't use --output_genotypes to obtain only 1 sample column in the VCF.
But I would like to keep the most frequent GT.
Question 1:
How can I obtain that? Is it possible or should I use the --output_genotypes and parse the results myself?
Else (with --output_genotypes ), I obtain several sample columns:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 0_sample1 1_sample1 2_sample1 3_sample1 4_sample1 5_sample1
Question 2:
Is there a way to report a tag associated to the input file where the SV comes from?
Something like:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
chr6 123605 . . <DEL> . PASS SVTYPE=DEL;SVLEN=200 GT:TAG 0/1:smoove,delly
If no, would it be possible to add an option --tag = a file listing tags associated to VCF files to merge (on separate lines).
Hello Melanie,
Thank you for providing this excellent tool ! Love it so much!
I'm currently using Jasmine to evaluate the presence/absence of SV identified with different SV callers in a small WGS cohort. Ultimately, I would like to obtain a single non redundant SV VCF with all the samples of my cohort:
.
I'm using Jasmine in 2 steps:
Step 1
For each sample of my cohort : I merge the SVs called with different SV callers (the idea is to determine all SV in a sample, considering all SV type, but without redundancy due to fuzzy coordinates) in order to obtain a unique VCF file for each sample.
=========Jasmine======> sample1_SV_merge.vcf
Wanted SV clustering criteria: => e.g. a maximum of 300bp distance between breakpoints and at least 80% reciprocal overlap by size.
Those are the parameters that I'm using:
I don't use
--output_genotypesto obtain only 1 sample column in the VCF. But I would like to keep the most frequent GT. Question 1: How can I obtain that? Is it possible or should I use the--output_genotypesand parse the results myself? Else (with--output_genotypes), I obtain several sample columns:Question 2: Is there a way to report a tag associated to the input file where the SV comes from? Something like:
If no, would it be possible to add an option
--tag= a file listing tags associated to VCF files to merge (on separate lines).<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">
File | Tag -- | -- sample1_SV_smoove.vcf | smoove sample1_SV_delly.vcf | delly sample1_SV_CNVpytor.vcf | CNVpytor sample1_SV_Manta.vcf | Manta sample1_SV_Mobster.vcf | Mobster sample1_SV_ExpansionHunter.vcf | ExpansionHunter