How to get a vcf output from SV calling pipeline?

NGSEP / NGSEPcore

NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions, deletions, and genomic regions with copy number variation (CNVs).

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How to get a vcf output from SV calling pipeline? #46

Closed kcleal closed 11 months ago

kcleal commented 1 year ago

Hi, Thanks for the nice tool chain. Ive run the SV calling pipeline but no vcf file is produced, only a gff file. How do I obtain a vcf file? My command was:

java -jar NGSEPcore_4.3.1.jar SingleSampleVariantsDetector -runOnlySVs -i sample.cram -r ref.fasta -o samp -runLongReadSVs -sampleId samp

ngaitan55 commented 10 months ago

Hi Kez, I appreciate your interest. I see you closed the thread but still, it is worth noting that version 4.3.2 now provides a vcf including only SVs with the parameters you used. Please let us know if you have further questions about the functionality.