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ahernank
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Apr 7, 2026
docs/af1/af1.1.ipynb
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| "## Whole-genome sequencing and variant calling\n", | ||
| "\n", | ||
| "All samples in `Af1.1` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " | ||
| "All samples in `Af1.1` (except for the samples in 1236-VO-TZ-OKUMU-VMF00248 and the samples in small-2020-af) have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. All samples in 1236-VO-TZ-OKUMU-VMF00248 have been sequenced individually to high coverage by Novogene. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " |
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| "All samples in `Af1.1` (except for the samples in 1236-VO-TZ-OKUMU-VMF00248 and the samples in small-2020-af) have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. All samples in 1236-VO-TZ-OKUMU-VMF00248 have been sequenced individually to high coverage by Novogene. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " | |
| "Most samples in `Af1.1` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. Exemptions are samples in `1236-VO-TZ-OKUMU-VMF00248` which have been sequenced individually to high coverage by a commercial provider, and samples in `small-2020-af` which have been curated from the literature [ref]. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " |
Could we trickle down something like this to the guides below?
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Thanks @ahernank, that makes a lot of sense. Are they exemptions or exceptions?
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I did the Ag sample sets as well at the same time and harmonised a bit more how the literature sample sets are presented. |
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Addresses #126.
I am not sure what I said is accurate or detailed enough.