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Invalid VCF record #25

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rrfuentes opened this issue Nov 12, 2021 · 2 comments
Open

Invalid VCF record #25

rrfuentes opened this issue Nov 12, 2021 · 2 comments

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

@rrfuentes
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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

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@rrfuentes @fangli80