variant IDs when using VG RNA and VG CALL

Question

[AshleeThomson]

Hi, I'm currently creating an exon only spliced graph (NOT haplotype specific) using vg rna, and wanted to know if there was a way to make the IDs (contigs) the chromosome number instead of the transcript ID. I understand that when using vg rna there is an option to input a transcript file

-n, --transcripts FILE     transcript file(s) in gtf/gff format

and the option to select which attribute tag to use as the ID

-s, --transcript-tag NAME  use this attribute tag in the gtf/gff file(s) as id [transcript_id]

but I want to use the chromosome number as the ID tag.

Currently when I use vg call on my graph, my VCFs look like this

##contig=<ID=ENST00000584536_R1,length=804>
##contig=<ID=ENST00000550993_R1,length=438>
##contig=<ID=ENST00000490417_R1,length=952>
ENST00000196061_R1  2489    >376099>117009861   T   C   15.5976 PASS    ...
ENST00000196061_R1  2640    >376103>118173663   T   C   12.7808 PASS    ...
ENST00000196061_R1  2662    >376104>105813788   A   T   12.5346 PASS    ...

But I want this format:

##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chr10,length=135534747>
1    10560   .       C       G       21.77   .       ...
1    13813   .       T       G       30.78   .       ...
1    14464   .       A       T       36.31   .       ...

Is there a way around this? Or is this specific to vg rna? My current code for vg rna is:

vg rna -p -d -o -r -n chr${i}.gtf chr${i}.vg > ${GRAPH_PREFIX}_${i}.vg

Any advice is welcome, and thanks in advance.

Answer 1

[AshleeThomson]

For those having the same issue and wanted to follow up, I just got a good reply on the VG Github page.

https://github.com/vgteam/vg/issues/3794