Not getting any results after merging VCFs

[poddarharsh15]

Hi @starskyzheng

I’m using PanPop under a Conda environment to merge structural variant (SV) VCF files. These VCF files had previously been merged using bcftools as I’m working with multiple samples. Unfortunately, I’m not getting any results after running the commands as outlined below.(only vcf headers in the vcf files)

Could you kindly provide some suggestions on how I might resolve this issue? I’m attaching my merged VCF files along with the code I used for reference.

1.bcftools merge -m none -o bcftools.vcf.gz 140528_D00360_0018_AH8VC6ADXX.vcf.gz 140528_D00360_0019_BH8VDAADXX.vcf.gz 140605_D00360_0020_AH9V1RADXX.vcf.gz 140605_D00360_0021_BH9V1VADXX.vcf.gz 140609_D00360_0023_BH9UD5ADXX.vcf.gz

2. 
   perl ~/structural_varinats/panpop/panpop/bin/PART_run.pl --in_vcf bcftools.vcf.gz -o OUTDIR_RUN1 -r /home/tigem/h.poddar/short_reads_pipelines/ref_genome/GRCh38/GRCh38.primary_assembly.genome.fa -t 16 --tmpdir TMPDIR

perl ~/structural_varinats/panpop/panpop/bin/PART_run.pl --in_vcf OUTDIR_RUN1/3.final.vcf.gz -o OUTDIR_RUN2 -r /home/tigem/h.poddar/short_reads_pipelines/ref_genome/GRCh38/GRCh38.primary_assembly.genome.fa -t 16 --tmpdir TMPDIR -not_first_merge

Thank you in advance for your help!

> input

[bcftools.vcf.gz](https://github.com/user-attachments/files/17013678/bcftools.vcf.gz)
[truvari_merge.vcf.gz](https://github.com/user-attachments/files/17013680/truvari_merge.vcf.gz)

[starskyzheng]

https://github.com/starskyzheng/panpop?tab=readme-ov-file#standalone-entry-for-part Noted REF, ALT and GT (colunm 4, 5 and 9) need to be completed in the VCF file. (see https://github.com/starskyzheng/panpop/issues/18)

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