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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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important_regions bed #203

Closed skose82 closed 1 year ago

skose82 commented 1 year ago

Hi there,

I have a few questions running smoove/Lumpy for the first time.

  1. For the following command in samplot vcf:

samplot vcf --filter "SVTYPE == 'DEL' & SU >= 8" --filter "SVTYPE == 'INV' & SU >= 5" --vcf example.vcf -d test -O png --important_regions regions.bed -b sample1.bam sample2.bam sample3.bam > samplot_commands.sh

Is the important regions bed required? Is this the same as the exclude bed file found here: https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed

  1. If not is there a recommended bed file to use for this?

  2. Is there any further information as to why SU is set to >= 8 and INV >= 5?

Many thanks

brentp commented 1 year ago

Hi, it seems this is more of a question for samplot. I don't think the --important_regions is required. You likely don't want to use the exclude file for that argument. I don't know where you got this example command, but it might be just an example. hope that helps. -B

skose82 commented 1 year ago

Much appreciated will check with samplot devs.