Aleks S Data Analyst UKB Community team

Member since 30 November 2023 06:08

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Last activity 11 January 2024 01:30

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Latest activity by Aleks S

Aleks S commented, 02 March 2023 12:55
Hi Emanuele, The extra WGS chunks come from small 5kb blocks on chromosomes 4 and 10. There is an excellent post by Rob Denroche in this thread: https://community.dnanexus.com/s/question/0D5t00000...
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- 02 March 2023 12:55
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Aleks S commented, 02 March 2023 12:46
Hi Andrew, The data comes from this field: https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=24304 Here is a good reference on the pVCF format and how it differs from gVCF:https://www.biorxiv.org...
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- 02 March 2023 12:46
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Aleks S commented, 14 November 2022 17:07
The data comes from this field: https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=24304 The pipeline used to produce this data is well documented in Nature publication: https://www.nature.com/art...
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- 14 November 2022 17:07
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Aleks S commented, 08 March 2022 11:19
Hi Fran, Could you explain what kind of project would you like to do and why you need to re-align the dataset? The alignment will be a considerable compute cost, significantly higher than UKB acce...
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- 08 March 2022 11:19
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Aleks S commented, 08 March 2022 10:56
Hi Fran, Yes, the chrUn_GL000220v1 contig is present in CRAM files available at RAP. Once you have access to CRAMs you can check which contigs are included using `samtools idxstats` Best wishes,Aleks
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- 08 March 2022 10:56
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Aleks S commented, 08 March 2022 10:45
Hi Fran, BWA is a great general purpose aligner and I highly recommend using it. For basic alignment stats `samtools flagstat` is a great option. You can find the manual page here: http://www.htsli...
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- 08 March 2022 10:45
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