variant IDs when using VG RNA and VG CALL
Entering edit mode
10 months ago

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

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:

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.

vg call rna variant • 425 views
Entering edit mode
10 months ago

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


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