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WGLab / LinkedSV

MIT License
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Invalid VCF record #25

Open rrfuentes opened 3 years ago

rrfuentes commented 3 years ago

Hi, I'm getting this error when running LinkedSV on my data. ERROR! invalid VCF record: NaN DPlow _DP=-1;undefined Can you kindly help me resolve it? Thanks!

fangli80 commented 3 years ago

Can you please provide a short description of your data and your command ? Thanks

rrfuentes commented 3 years ago

This is the command I used python /linkedsv.py -i data.bam -d dir/ -r ref.fa -t 30 --somatic_mode --black_region_bed LinkedSV_blackregion_empty I also got this error message at the end FileNotFoundError: [Errno 2] No such file or directory: 'dir/discordant_read_pairs.del.bedpe'

I am trying to detect SVs in tomato genome using 10x reads.

Thanks