smoove
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brentp
structural variant calling and genotyping with existing tools, but, smoothly.
When i try: [smoove annotate --gff $gff3 join_call.smoove.square.vcf.gz | bgzip -c > join_call.smoove.square.anno.vcf.gz ] It always give me: [smoove] 2022/02/17 11:08:27 starting with version 0.2.5 hangup I don't know the...
Hi, @brentp, @lindenb Thanks for your great work ! There was a problem with the annotation ``` smoove annotate --gff silkie_end.gff3.gz 26indiv_ZW-smoove.genotyped.vcf.gz | bgzip -c > 26indiv_ZW-smoove.genotyped.anno.vcf.gz (smoove) [poultrylab1@pbsnode01 sk_as_ref_118_indev_bam]$...
Dear professor, Thanks a lot for such a good comprehensive tool. can you help to me to look at this question? with or without gff both does not work; I...
Hello @brentp, I ran smoove like this --- `smoove call --name ${sample} -x --exclude ${blist_region} --fasta ${FASTA} -p 3 --outdir ${sample}_smoove --genotype ${bam_path} ` and the following logs were generated...
Hello, I run smoove v.0.2.6 within a pipeline https://github.com/antonkulaga/dna-seq, in a container. To the moment I got two different samples ended up with the same error result. Input bam sequence...
index error
Hi, I'm running smoove from docker (in wdl). With large bam files everything goes smoothly (and so fast!), but I get the following error (from times to times) when the...
The lumpy_filter command used by `smoove call` uses 2 threads, regardless of the `--processes` argument given to `smoove call`. Observing the running processes shows around 5-10% cpu utilisation. Testing the...
Hi, I ran Smoove using a population calling mode. There is a duplication shared by >10 samples however, Smoove detected this in none of the samples likely due to low...
Hi, I ran into a problem with smoove merge smoove merge --name merged -f /public/home/reference_fa/LYC_chr.fasta --outdir /public/home/smoove_test/merged_vcf /public/home/smoove_test/bam/*.vcf.gz [smoove] 2021/10/09 18:25:38 starting with version 0.2.8 [smoove] 2021/10/09 18:25:38 merging 2...
Hello, I would like to use this tool in an haploid organism. It would be possible? If so, what parameters should I modify? Thanks Pablo
