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Hi !
I am trying to generate VCF from the GFA produced by the PGGB pipeline.
I attempted to use `deconstruct`, and everything works fine on smaller GFA files, such as when I only include two species…
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Hi Ryan,
Do you have any recommendations on how I can filter the VCF file, I mean which parameters? As all the calls are listed imprecise, I wanted to filter it. Also, the PRPOS and PREND listed in t…
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Following the example (below) to generate tumor_normal.vcf file, it seems lumpy generated many more somatic SVs than other tools. Do you have any suggestion for filtering some low quality calls from…
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For discussion:
# Specification: VCF to VRS Processing Package with Cohort Allele Frequency Generation
## Overview
This package processes Variant Call Format (VCF) files to ensure compatibility…
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### Description of feature
Generate tumour-only mode for variant calling. This should only affect to the `variant_calling` module of the pipeline, once we obtain the VCFs the rest of modules should b…
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Next steps:
- [ ] change hairpin process to run within singularity image (shub://MathijsSanders/SangerLCMFilteringSingularity)
- [ ] build singularity image for vcf_flag_modifier.py (python packages…
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Hi,
I'm using dsc-pileup and freemuxlet to identify donors/doublets of a two-donor mixture. I pre-filter the bam file using the popscle_helper_tools (https://github.com/aertslab/popscle_helper_tool…
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Hi,
I would like to know what the vcf requirements are? Can it be .gz? Should previously filtering for only biallelic loci be done? I get a core dumped error using a vcf.gz with 7 individuals for a …
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I am working on calling variants in spatial transcriptomics data (10x Visium). Since the sequencing depth of spatial transcriptome is poorer than single-cell data, I want to treat all reads in the bam…
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[GA00_AO2_BB1_01_annotsv_new.bed.zip](https://github.com/user-attachments/files/17144001/GA00_AO2_BB1_01_annotsv_new.bed.zip)
@lgmgeo Hello, I am trying to use the web version of annotsv, and I appr…
lpsyy updated
1 month ago