PopGenome lost individual information

Question

[Yixuan]

Dear all,

I am new in PopGenome and facing some problems in importing myVCF file via readData function.

I have cut my full vcf.gz file in chunks by chromosome (also vcf.gz. 10 chromosomes in total) via bcftools. I later unzipped these chromosome vcf.gz files to vcf and stored them in one folder.This is because my R chrashes when handling vcf.gz files by readData fucntion. After reading the folder via readData, there are no information of individuals (e.g names) left. When I ran [e-mail]@populations2 [e-mail]@populations, it only returns NULL for each region. get.individual(my.vcf) also only returns NULL from each region.

The first few lines of my header looks like this:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT                          CbGer22-107                CbGer22-108
chr1    1363    .   A   G   284.59  .   .   GT:DP:SP:AD:SCR:QS:PL:NMBZ:GQ   0:41:0:41,.:0:1992,.:.:.:.  0:38:0:38,.:0:1604,.:.:.:.
chr1    3642    .   G   A   284.59  .   .   GT:DP:SP:AD:SCR:QS:PL:NMBZ:GQ   0:27:0:27,.:2:1180,.:.:.:.  0:18:0:18,.:0:846,.:.:.:.
chr1    5476    .   T   C   284.59  .   .   GT:DP:SP:AD:SCR:QS:NMBZ:PL:GQ   0:37:0:37,.:0:1610,.:.:.:.  0:34:0:34,.:0:1302,.:.:.:.
chr1    6585    .   G   A   284.59  .   .   GT:DP:SP:AD:SCR:QS:PL:NMBZ:GQ   0:26:0:26,.:0:1226,.:.:.:.  0:16:0:16,.:0:612,.:.:.:.
chr1    9043    .   A   G   284.59  .   .   GT:DP:SP:AD:SCR:QS:PL:NMBZ:GQ   0:33:0:33,.:0:1493,.:.:.:.  0:27:0:27,.:2:1100,.:.:.:.

Could you please help me with this issue? Did I do something wrong? Many thanks in advance.

Cheers,

Yixuan

[dthorbur]

Can you provide the first line of data in the VCF after the header? (i.e., line starting with #CHROM and 1 more)

[Yixuan]

Hi there, Thanks for the comment. I updated my question with the info you need. Cheers,

[kristensen1234]

Hi,

I am facing the same problem and was wondering if you found a solution?

[Arup Ghosh]

Can you share the command you are using?