if Indel can be used in VCF input now

Question

if Indel can be used in VCF input now

Opened this issue 5 years ago · 3 comments

Dear Natsuhiko,
I want to run rasqual on my data. Now I want to know,if Indel can be used in VCF input now.

XU

Answer 1 · 2019-03-13T09:25:22.000Z

Hi Xu,

RASQAUL can map QTLs with indel variants, but they are not used as feature variants. You need to set the AS counts in the VCF file as "0,0" for those indels.

Best regards,
Natsuhiko

Answer 2 · 2019-03-20T19:06:21.000Z

Dear Natsuhiko,

Thanks so much for developing rasqual!. I have a comment related to the indel question. When I run Rasqual with indels it seems that the reference and alternative columns only contain the first base of the indel. For example:
"chr1_27935068_27939883 rs71584896:27937602:T:TCACA chr1 27937602 T T 0.816667 1.511870 0.636000 -0.0436694743 0.0144441701 0.495650 0.000156 0.473767 36.907173 2 2 1 5 0 27937602 -164.078365 0 0.802343 0.411602"

Which at the end it shows that the reference and alt allele are the same.

best,

Ariel

Answer 3 · 2019-03-21T09:02:40.000Z

Hi Ariel,

Sorry for the inconvenience, RASQUAL was designed for mapping QTL SNPs in principle and the allele fields in VCFs are not fully scanned (only the first character is read). This problem will be solved in the next update.

Best regards,
Natsuhiko