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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why my NGSEP vcf output do not have any CNV information ? #16
Here is my commend line
nohup java -jar NGSEPcore_3.3.2.jar MultisampleVariantsDetector -r genome.fa -ploidy 6 -o compare.vcf ./sample.bam 2>log &
I could get many SNP position just like GATK UG caller output
But the "type=***" in my vcf output file with only indel ,and how should i get my "sample.bam" CNV position in the aliment file between my genome file ?
Here is my commend line
nohup java -jar NGSEPcore_3.3.2.jar MultisampleVariantsDetector -r genome.fa -ploidy 6 -o compare.vcf ./sample.bam 2>log &I could get many SNP position just like GATK UG caller output But the "type=***" in my vcf output file with only indel ,and how should i get my "sample.bam" CNV position in the aliment file between my genome file ?