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kcleal / dysgu

Toolkit for calling structural variants using short or long reads
MIT License
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TRA variants #34

Closed Akazhiel closed 2 years ago

Akazhiel commented 2 years ago

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 commented 2 years ago

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

kcleal commented 2 years ago

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 commented 2 years ago

Closing this for now

wenyuhaokikika commented 1 year ago

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 commented 1 year ago

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