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Windown labeling fails on CTX SV type #77
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The VCF file htz-sv.vcf generated by SURVIVOR simSV in sv-gen is malformed. I will open an issue in sv-gen. |
@lsantuari: Which of these TRA lines are you referring to? Lines 4020 to 6019 in 27a24d5
related to #76 |
All of them. Here is how the SVs should be in VCF format according to v4.3. |
It is working for CTX (which is the transformed TRA), so it should be enough in our case. |
OK, I'll remove this line. Line 20 in 02e22f0
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https://travis-ci.org/github/GooglingTheCancerGenome/sv-channels/jobs/745625564#L5094
It seems to relate to the TRA/CTX mismatch below:
sv-channels/scripts/genome_wide/label_windows.py
Line 66 in 6174d09
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