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Issue by @MaxUlysse, moved from SciLifeLab#666
- [ ] [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
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Hi,
I want to benchmark my variant calls (not GIAB or platinum dataset). How should i do with the help of this tool?
Thanks
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Hi, I was comparing some different VCF extraction packages and have been really impressed by the extraction speed in the h5 output of vcf_to_hdf5. However, I was doing some basic tests just to check o…
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i was unable to merge SvABA calls using SURVIVOR and I don't see any issues regarding SvABA, so this might be a new topic for this tool. My command is:
`SURVIVOR merge sample_files 100 1 0 0 0 50 sam…
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I'm interested in tracing previously identified somatic mutation for each single cell. am wondering if the souporcell_merged_sorted_vcf.vcf.gz contains only germline variants or it also contains somat…
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This is something to keep in mind when we start using this functionality.
_Originally posted by @jPleyte in https://github.com/GenomicsDB/GenomicsDB/pull/186#discussion_r794222104_
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If you are wedded to using Deflate, don't use Zlib as it's simply ancient technology. I'd advise [libdeflate](https://github.com/ebiggers/libdeflate/) instead as generally it's over double the perfor…
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Hi Simon,
referring to your paper here (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814882/), I have done a similar comparison between autosomal data and haploid sex chromosome data (homogametic in…
foala updated
3 years ago
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Thank you very much for developing this useful code. Does it work on targeted sequencing data too?
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I am trying to use the variant-utils comparetwo function to compare two gvcf files from our GATK pipeline. I have tried several iterations of files including converting to vcf using gvcftools (extrac…