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WGLab / NanoCaller

Variant calling tool for long-read sequencing data
MIT License
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extract whole genome SNP and haplotype #6

Open qiang-huang opened 3 years ago

qiang-huang commented 3 years ago

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 commented 3 years ago

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

umahsn commented 3 years ago

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 commented 3 years ago

I am eager to test the second option.

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From: umahsn notifications@github.com Sent: Monday, September 21, 2020 21:01 To: WGLab/NanoCaller NanoCaller@noreply.github.com Cc: qiang-huang qiang-huang@live.com; Author author@noreply.github.com 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.

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