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### Context
Originally requested by Katie on [Slack](https://bedfordlab.slack.com/archives/C0K3GS3J8/p1718398583181119).
Looking at [H3N2 with genotype coloring for 186, 190](https://next.nexts…
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Hello,
I have WGS sequencing data, incuding the bam files and the called SNPs as vcf. I used now stitch to impute my SNPs based on the bam files and the SNP positions. However, I realized since I am …
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The [VCF 4.4 spec](https://samtools.github.io/hts-specs/VCFv4.4.pdf) allows for an initial symbol indicating the phasing of the first allele. For example, `/0/1` is a valid genotype. This allows for p…
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Dear David:
Please refer to my post at PLINK users group:
https://groups.google.com/g/plink2-users/c/Xvt895jb48w
It seems that **there is no readl ChrY data from the UK Biobank genotype datas…
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Investigate a sparse encoding of genotype posteriors. E.g. an equivalent to the `PP` field (phred-scaled probabilities) in which zeoro values are omitted. This can be represented as a map of genotype …
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BAMfiles probably need to be QNAME sorted (rather than coordinate sorted) when splitting them
riasc updated
2 weeks ago
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using sample sheet as input. can span across multiple project folders.
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1000FARMS.climmob needs a consistent well document list of varieties/genotypes aligned with BMS https://bmspro.io
Also when the list becomes too long we need to develop an approach to select genot…
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The [VCF 4.4 spec](https://samtools.github.io/hts-specs/VCFv4.4.pdf) now allows for an initial symbol indicating the phasing of the first allele. For example, `/0/1` is a valid genotype. At present, v…
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Hi,
when i used the vg call to obtain the genotype file from short reads. I didn't know these genotype. for example,1/1,1/0,0/1 . These genotype were not including 0/0?