extract whole genome SNP and haplotype

[qiang-huang]

The tutorial provided the command to extract a specific region of SNP and haplotype. If I want to extract ALL the SNP and haplotype of the genome, how to set -chrom parameter? I tried "-chrom None". It does not work.

[umahsn]

-chrom is a required flag. You would need to run the command separately for each chromosome.

[umahsn]

We have added two methods for whole genome variant calling. 1) We write the commands needed to run NanoCaller on each contig into a file. You can then use whatever method of parallel computing or job submissions to a cluster to run these commands. This is preferable mode of running. 2) Instead of printing the commands for each contig, in the second mode NanoCaller will just call variants in each contig in a sequence. We have also added several ways of specifying what contigs you want to use in whole genome mode.

[qiang-huang]

I am eager to test the second option. 发送自 Outlook<http://aka.ms/weboutlook>

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________________________________ From: umahsn <[email protected]> Sent: Monday, September 21, 2020 21:01 To: WGLab/NanoCaller <[email protected]> Cc: qiang-huang <[email protected]>; Author <[email protected]> Subject: Re: [WGLab/NanoCaller] extract whole genome SNP and haplotype (#6) We have added two methods for whole genome variant calling. 1) We write the commands needed to run NanoCaller on each contig into a file. You can then use whatever method of parallel computing or job submissions to a cluster to run these commands. This is preferable mode of running. 2) Instead of printing the commands for each contig, in the second mode NanoCaller will just call variants in each contig in a sequence. We have also added several ways of specifying what contigs you want to use in whole genome mode. ― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FWGLab%2FNanoCaller%2Fissues%2F6%23issuecomment-696308880&data=02%7C01%7C%7C346002aadeda4708403808d85e60c8d7%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637363117080601018&sdata=nJ5WyxXSyi%2BZTpJwKtnWMfZKEK0BoXFuV0LwzQMTSoo%3D&reserved=0>, or unsubscribe<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAES62YPJ4GXAEJ7MAGIGVTTSG6PJRANCNFSM4RE7ZCLQ&data=02%7C01%7C%7C346002aadeda4708403808d85e60c8d7%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637363117080611011&sdata=uWhFPyqwFbiBQCJnEvofzov%2BXrMIJp%2BnG7g6eA26bsU%3D&reserved=0>.