Probblem converting VCF to Joinmap format

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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Probblem converting VCF to Joinmap format #3

Closed avdanurag closed 5 years ago

avdanurag commented 5 years ago

Hi, I am trying to convert VCF file (generated using taasel 5) in to join map format but output only contains header. Please look in to this issue. Here is my command

java -jar NGSEPcore_3.3.0.jar ConvertVCF -printJoinMap -p1 PB1.CEL_call_code -p2 SS.CEL_call_code trail_rice.vcf trail_rice_geno

jduitama commented 5 years ago

Hi @avdanurag

My apologies for the delayed answer. I thought it was the same issue reported in sourceforge. Would you mind sharing the first few variants in your VCF to try to reproduce the issue?. Make sure that you have homozygous differences between your parental lines. You can run the filter command selecting only the two parents and the option -fi and see if you still get variants.

Best regards

Jorge