search

arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
307 stars 119 forks source link

lumpyexpress produce no CNV output #330

Open swu13 opened 4 years ago

swu13 commented 4 years ago

Hi,

I use lumpyexpress to detect CNV in the sample (the code is shown below), but I got no CNV in NA12878.vcf which seems not right. I only got some DEL, DUP,... Is something not correct?

samtools view -b -F 1294 NA12878.bam > NA12878.discordants.unsorted.bam samtools view -h NA12878.bam | extractSplitReads_BwaMem -i stdin | samtools view -Sb - > NA12878.splitters.unsorted.bam samtools sort NA12878.discordants.unsorted.bam -o NA12878.discordants.bam samtools sort NA12878.splitters.unsorted.bam -o NA12878.splitters.bam lumpyexpress -B NA12878.bam -S NA12878.splitters.bam -D NA12878.discordants.bam -o NA12878.vcf

Thank you!

ryanlayer commented 4 years ago

I am not sure I understand the issues. DEL and DUP are CNVs.