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Hi,
Thanks for developing this nice tool.
I have two genomes, assembly1 and assembly2. My goal is to use these two genomes as reference genomes, align reads to each of them, and call variants. T…
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**Description:**
I am encountering an issue when trying to convert a VCF file to BGEN format using the Glow library on Databricks in Azure.
**Context:**
I am using the following code to read a V…
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Hello,
I am trying to use a variation genome graph to genotype SVs on more samples sequenced with short-reads, and I'm trying different avenues (see 1)graph from vcf + giraffe and 2) graph with pggb+…
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( bedtools v2.25.0-70-g577fecf )
I try to intersect a vcf.gz with a vcf resulting from another bedtools subtract run
run#1: bedtools intersect -a ${afile} -b ${bfile} > ${outfolder}/common_ab.vcf ; #…
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Dear developer,
I compared trueset file NA12877.vcf.gz( including SNP and IDNEL variants) with query file(only SNP variants). For the INDEL in summary.csv, there are numbers on TRUTH.TP TRUTH.FN col…
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I re-aligned the [HG002 30x PCR-free WGS BAM from Baid et al](https://console.cloud.google.com/storage/browser/brain-genomics-public/research/sequencing/grch38/bam/novaseq/wgs_pcr_free/30x) against hs…
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```
cat 2202415007_hemi.vcf | head
/home/zmvanw01/projects/12-sample-comparison/hifiasm-path/geno_analysis/per_samp/2202415007/change_to_hemi/2202415007_hemi.vcf
=mpileup -B -a QS -Ou -f /home…
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I am currently doing benchmarking of the VCF files with the gold standard file **HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf**. Whil…
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The need for unit tests for SLiM's popgen functions has been underlined by another discovery of a bug with them (https://groups.google.com/g/slim-discuss/c/Yacfk9EIYeU/m/bc72wVUzBAAJ). I'm not sure h…
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Hi, what about publishing the bamsurgeon Docker image on GitHub Container Registry:
https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry