Hello, I am reaching out because I am working on understand GATK-SV but part of the code is confusing me. When I run ResolveManta on of the clusters consists of the two following records
chr1 88507142 manta_NA12878_285 N N]chr17:88507142] . PASS SVTYPE=BND;CHR2=chr17;STRANDS=++;SVLEN=-1;ALGORITHMS=manta;EVIDENCE=PE;MEMBERS=manta_NA12878_285 GT:manta 0/1:1
chr1 88507127 manta_NA12878_284 N [chr17:88507127[N . PASS SVTYPE=BND;CHR2=chr17;STRANDS=--;SVLEN=-1;ALGORITHMS=manta;EVIDENCE=PE;MEMBERS=manta_NA12878_284 GT:manta 0/1:1
This cluster gets called as a CANDIDATE_TRANSLOCATION, which then calls get_arms(). I see get_arms() uses the stop position of the SV, however the stop position of these looks wrong as there is no END field in the info column and the base position on the other chromosome is the same as the initial chromosome, which must be wrong since chromosome 17 isn’t that long. I believe this is why the code is crashing when I try to run it. Do you have any idea how I can fix this problem?
Hello, I am reaching out because I am working on understand GATK-SV but part of the code is confusing me. When I run ResolveManta on of the clusters consists of the two following records
This cluster gets called as a CANDIDATE_TRANSLOCATION, which then calls get_arms(). I see get_arms() uses the stop position of the SV, however the stop position of these looks wrong as there is no END field in the info column and the base position on the other chromosome is the same as the initial chromosome, which must be wrong since chromosome 17 isn’t that long. I believe this is why the code is crashing when I try to run it. Do you have any idea how I can fix this problem?
Thank you very much.