prasundutta87

Results 44 comments of prasundutta87

query about force calling in sniffles v2.0.6

Thanks @fritzsedlazeck . I am aware that this is the multisample calling feature and that's my goto method in sniffles2 SV calling. I was just trying out the force calling...

No AF value in multisample VCF file

Thanks for confirming this @wdecoster ! Hi @fritzsedlazeck ! I was mentioning the missing AF values for a multisample VCF file (trio in my case). Regards, Prasun

query about using multisample variant calling/genotyping feature

Thanks @fritzsedlazeck . I believe that the snf file making step is very important for the multisample SV calling and this is different from force calling feature where I can...

query about using multisample variant calling/genotyping feature

Thanks for your reply to my queries @fritzsedlazeck. Regarding ./., are you pointing towards --min-support option (whose default is 10)?

query about using multisample variant calling/genotyping feature

Thanks a lot, @fritzsedlazeck !

query about --minsvlen parameter

Thanks @fritzsedlazeck ! I guess, I can put a filter downstream to retain variants where SVLEN > 50 and SVLEN < -50. Then it will truly include all 5 types...

query about 0/0

Thanks for confirming this, Fritz! I will be working with human trios to get clinically relevant SVs. Just wondering what kind of experiments or organism will need to keep 0/0.

query about 0/0

Thanks for your help, Fritz!

SV calling on sex chromosomes

Thanks for this @fritzsedlazeck ..will keep you posted! Regards Prasun

query about PED and trio VCF

Thanks @brentp !