smoove
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brentp
structural variant calling and genotyping with existing tools, but, smoothly.
Hello, I am trying to run Smoove following instructions and really basic paramètres and just one bam file but I am running into an issue at lumpy-filter stage called "exit...
Hi, I am trying to run `smoove call` on a set of matched normal-tumor bam files. I've properly run it on more than 100 WGS samples belonging to a dataset,...
@brentp Smoove is not working even after my bam size is quite good. Command used: smoove call --outdir test_mansi/SRR6745447_output/smoove_output/ --name SRR6745447 --fasta part_II/references/hg38.fa -p 1 --genotype part_II/output/fq2bam_no_indels/SRR6745447_sorted.bam The size of...
I used singullarity to run smoove, but met below info and the job was killed. Do you konw the reason? something wrong with bam header? how to fix this? Thanks...
> [smoove] 2022/04/27 15:54:53 starting with version 0.2.8 > panic: sam: duplicate program name: line 3430: "@PG\tID:SAMBLASTER\tVN:0.1.24\tCL:samblaster -i dummy.cram.readsorted.sam -o dummy.cram.samblster.sam --addMateTags" > > goroutine 1 [running]: > github.com/brentp/smoove/lumpy.check(...) >...
Hi all, I'm trying to run this command (from inside a docker container): ``` smoove call --outdir /work/home/results-smoove-chr1/ --exclude /work/home/exclude.cnvnator_100bp.GRCh38.20170403.bed --name SP0184750 --fasta /work/home/GRCh38_full_analysis_set_plus_decoy_hla.fa -p 1 --excludechroms '~^GL,~^HLA,~_random,~^chrUn,~alt,~decoy,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM' --genotype s3:///...
Hi, thanks a lot for the development of this tool. I am trying to use smoove for a triticum genome and the program give an error saying that it cannot...
Hi， I ran smoove pipeline on ~4500 WGS samples and I found 102980 SV including 71367 DEL. The percentage of DEL is too high. I found the percentage of DEL...
Good afternoon, I've been trying desperately to annotate my final vcf file as the last step for smoove, using genome version hg38. However, when I use the gencode gff3 file,...
Hi, I'm having a weird parsing time issue when running smoove call on individual WGS cram (same on converted bam) samples (running it on population cohort): ``` singularity run /dcsrsoft/singularity/containers/smoove-0.2.7.sif...