gevro
gevro
Hi, ProcessRepeats crashed on our computing cluster due to 'out-of-memory'. So now I'm running ProcessRepeats separately on the final cat file (3.9 Gb). However, there is no indication of progress...
Hi, Are there reference files available to perform imputation on CHM13-v1 aligned data? Also, would QUILT work on high-cvg (~35x) whole genome sequencing, to help find the very small number...
Hi, The new AnnotSV VCF output format has an issue -- many numeric fields are being given Type=String. This breaks downstream pipelines that then do not allow proper numeric type...
GATK version: 4.4.0.0 Crashing in FilterAlignmentArtifacts. Not clear why Command ``` java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx30g -jar /gpfs/data/lab/bin/gatk/gatk-package-4.4.0.0-local.jar FilterAlignmentArtifacts -R /gpfs/data/lab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta -V 60603-bulk.filtered.vcf.gz -I /gpfs/data/lab/projects/Mini/analysis/STR/60603-bulk_results/60603-bulk.cram --bwa-mem-index-image /gpfs/data/lab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta.img -O 60603-bulk.filtered.FAA.vcf.gz...
Hi, We're getting the below error, near the end of the pipeline. Any idea what the issue is? Thanks ``` You provided these parameters: YAML file: RNAseq_4-17-23.yaml zUMIs directory: /gpfs/data/lab/bin/zUMIs...
Hi, I made a docker with zUMIs, and I got past the prior error, but now getting this error. I'm running it as a singularity image, so I know that...
Hi, Is the output BAM contain all UMI reads from each molecule, or only one UMI-collapsed read from each unique UMI molecule? If the former, is there a way to...
Hi, My methylationstats profile doesn't look like what is in the vignette. Is this a computational issue or does this suggest a specific sample issue? Thanks
Hi, What is the difference between: CallOverlappingConsensusBases tool vs "consensus-call-overlapping-bases" in CallDuplexConsensusReads tool ? The former tool has two options: agreement-strategy and disagreement-strategy But these options are not available in...
Hi, Your best practices has two options: Filteringconsensusreads before, and Filteringconsensusreads after mapping the consensus reads. https://github.com/fulcrumgenomics/fgbio/blob/main/docs/best-practice-consensus-pipeline.md Are these functionally equivalent? Any reason for one vs the other? Thanks.