edgarsierraorozco

Hello, While trying to cal SVs from a Lumpy output, I receive this error: Error: invalid FORMAT field, "+" Here is my code: /Library/Python/2.7/bin/svtyper -B LA1303_int2sort.bam -i LA1303_lumpy.vcf > LA1303_svtyper.gt.vcf...

I am trying to use HALC to correct long reads. I get this output that I haven't figured out how to use: [e.sierra@login3 output]$ head HALC.corrected.fa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

Hello, I ran Lumpy to find SVs in a tomato sample. As the Github page recommends, I tried using SVtyper to call the variants. However, I receive this issue: Error:...