I am running into an issue with multisample calling for BND variants. I am merging two samples together.
Both of the following lines are in the multisample vcf, even though they correspond to the same variant:
chr1 126647803 Sniffles2.BND.632M0 N N]chr7:98078765] ... SUPP_VEC=01
chr7 98082316 Sniffles2.BND.534M6 N N]chr1:126644102] ... SUPP_VEC=11
I would expect there to only be a single line with SUPP_VEC=11.
The first sample has the following lines:
chr7 98082316 Sniffles2.BND.3D13S6 N N]chr1:126646467] ... GT:GQ:DR:DV 0/1:13:13:5
The second sample has the following lines:
chr1 126647802 Sniffles2.BND.944CS0 N N]chr7:98078765] ... GT:GQ:DR:DV 0/1:4:3:9
chr7 98082316 Sniffles2.BND.6584S6 N N]chr1:126645438] ... GT:GQ:DR:DV 0/1:47:19:10
I believe that chr1:126645438 should actually be chr1:126647802 due to an error from a hard clipped read (as in https://github.com/fritzsedlazeck/Sniffles/issues/409 which I believe might be the underlying issue in https://github.com/fritzsedlazeck/Sniffles/issues/359). I also believe that chr7:98078765 should actually be chr7:98082316 due to an error from a hard clipped read. These errors are contributing to the fact that there are multiple lines in the vcf file for the second sample, when there should only be one.
I am not sure if that is the only problem, but I also wonder whether the order of the two chromosomes in the vcf line is preventing a correct merging. For example, does Sniffles correctly merge the following:
Hello,
I am running into an issue with multisample calling for BND variants. I am merging two samples together.
Both of the following lines are in the multisample vcf, even though they correspond to the same variant:
I would expect there to only be a single line with SUPP_VEC=11.
The first sample has the following lines:
The second sample has the following lines:
I believe that chr1:126645438 should actually be chr1:126647802 due to an error from a hard clipped read (as in https://github.com/fritzsedlazeck/Sniffles/issues/409 which I believe might be the underlying issue in https://github.com/fritzsedlazeck/Sniffles/issues/359). I also believe that chr7:98078765 should actually be chr7:98082316 due to an error from a hard clipped read. These errors are contributing to the fact that there are multiple lines in the vcf file for the second sample, when there should only be one.
I am not sure if that is the only problem, but I also wonder whether the order of the two chromosomes in the vcf line is preventing a correct merging. For example, does Sniffles correctly merge the following:
Thanks for your help.