TRA variants

[Akazhiel]

Hello,

Is there any option to output the Translocations according to the VCF specifications? Meaning 2 entries per translocation and the alternate allele in this fashion ]chr18:53456042]N ?

Best regards,
Jonatan

[kcleal]

Hi @Akazhiel,
There is no option for this currently, although I think this should be simple to add. I will get this added

[kcleal]

I have uploaded a script that converts target svtype(s) to BND format (see scripts folder). It can be used as follows:

python3 convert2bnd.py -t TRA reference.fa input.vcf > output.vcf

[kcleal]

Closing this for now

[wenyuhaokikika]

I have uploaded a script that converts target svtype(s) to BND format (see scripts folder). It can be used as follows:

python3 convert2bnd.py -t TRA reference.fa input.vcf > output.vcf

hello, where is the convert2bnd.py script please ? thank you ~~~

[kcleal]

My apologies, that folder seems to have gone missing. Ive added it back on the dysgu_dev branch. I will get it merged wihth the main repo in a few days:

https://github.com/kcleal/dysgu/tree/dysgu_dev