Marghoob Mohiyuddin

@pavanstrand thanks for this. Did you run this branch on the data to ensure that the output VCF is identical to output before formatting?

@pavanstrand looks good to me. Did you check to see if the output from 1 thread now is the same as earlier?

👍

@msahraeian please have a look at the comments. Thanks.

@roger-liu-bina @yunfeiguo what changes would this require?

Not entirely sure what is going on. It might be related to the variant normalization approach. Let me have a look and see if I can reproduce it (and hopefully...

It would be great if you can share the VCF.

Many thanks for pointing out the bugs @hh1985 ! We will fix this as soon as possible.

@yunfeiguo was this fixed?

Thanks @choosehappy! I've made a note of this and will have a fix soon.