smoove
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brentp
structural variant calling and genotyping with existing tools, but, smoothly.
Hi, I'm trying to run smoove using the docker container. I have 12 BAM files with different read length (50 and 86). 0 reads were removed during the filtering phase....
Hi, FYI, when using /smoove-0.2.6 + singularity. With `smoove genotype ` , some variants have POS>INFO/END. command: ``` singularity exec\ --home \${PWD} \ --bind ${bam.getParent()}:/bamdir \ --bind ${vcf0.getParent()}:/mergeddir \ --bind...
Hi, I ran into a problem with smoove paste # smoove paste --name RHF *joint-smoove.genotyped.vcf.gz [smoove] 2021/08/02 12:52:45 starting with version 0.2.6 [smoove] 2021/08/02 12:52:45 squaring 25 files to RHF.smoove.square.vcf.gz...
Hi, I am calling CNVs at sequence depth of ~10X. There are almost no small duplications (~100bp) in callset . But I could find small deletions. Is it normal? I...
I ran smoove annotate and got this error (below). But the smoove.square.anno.vcf.gz was generated. When I ran bcftools stats the anno file had 1 less record than the input vcf....
Hello, I'm trying to run smoove call on a cohort of 10-25 WGS samples sequenced to 20X coverage. Species is disploid and genome size ~2G. I have 65G memory. Memory...
Hi Brent, We have a collection of Structural Variant VCF files produced by Illumina Dragen. These are per sample, not yet in a multi-sample "squared off" format. I tried to...
Hi, I'm doing population calling and made it to the genotype step. There's 25 samples, similar coverage (20X). The first handful of samples finished quickly (1hr). This is the command...
hi @brentp tried recompiling the Smoove package with all the dependency found these issues and help on this would be great ``` smoove version: 0.2.7 smoove calls several programs. Those...
Dear @brentp I used the following command to run Smoove on my several thousands of samples: $SMOOVE call --outdir $OUTDIR --exclude $BED --name $ID -f $REF -p 1 --genotype $BAM...
