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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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'0/1' genotypes a vcf generated with SingleSampleVariantsDetector a -ploidy 1 option #33

Closed Acanthodasha closed 3 years ago

Acanthodasha commented 3 years ago

I'm sorry, could you suggest, why after genotype calling of a haploid organism with SingleSampleVariantsDetector with -ploidy 1 option the resultant .vcf contains '0/1' genotypes, please? I've used the following command: ngsep SingleSampleVariantsDetector -runRep -runRD -runRP -minQuality 30 -ploidy 1 -sampleId {some sample Id} -r {reference} -i {input} -o {some sample}_Q30 Such genotypes are also present in Demo_ann_q40_s_fi_I2_noREP_noCNV.vcf. I've done calling on the same bam file with another caller, and it tends to render the genotypes at the same positions as '1' in the vcf, but I want to use ngsep. I've done genotype calling from the same bam file using another caller, and it tends to render genotypes at the corresponding positions as '1', but I want to use ngsep.

jduitama commented 3 years ago

This issue was solved at our FAQ at sourceforge: https://sourceforge.net/p/ngsep/discussion/faq