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Need help to separate a genome in different x coverage

We are developing a pipeline to identify plant SNPs and Structural variations. As a part of checking, we have to separate a plant genome in different X coverage. For instance, actual genome data coverage is 40 X, now we need to generate it in different X coverage like 10X, 20x and 30x. Is it possible? If yes please help me.

plant genome x coverage normalization
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updated by Vitis Vitis • written by ashokkumar.mb • ashokkumar.mb

Thank you so much

Yes, I would like to do downsample our genome coverage. I read BBTools guide and found a command to do downsample "bbnorm.sh in=reads.fq out=normalized.fq target=100 min=5". Do I need to concern about any other parameters in this? or Do I need to do use any other tool to downsample genome data after this bbnorm?

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written by ashokkumar.mb • ashokkumar.mb

If this is what you would like to do, then I think for your purposes, you can simply do:

bbnorm.sh in=reads.fq out=normalized-30x.fq target=30 min=5
bbnorm.sh in=reads.fq out=normalized-20x.fq target=20 min=5
bbnorm.sh in=reads.fq out=normalized-10x.fq target=10 min=5

And then re-run our SNP- and Structural-calling pipeline to see the results with normalized-30x.fq, normalized-20x.fq, normalized-10x.fq. Granted that is assuming that is what you want to do: downsample the reads and see how it affects SNP and Structural calling.

Note: you might want to limit memory using the -Xmx200g (to limit to max 200GB RAM for example) and add threads=num_cores_on_your_computer. By default, I think bbnorm.sh uses 85% of RAM and all cores.

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written by jean.elbers jean.elbers

See Split BAM by average coverage .

When calling SNPs and indels with samtools / bcftools, the resulting vcf file will include each variant coverage.

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written by h.mon h.mon

1 answer

If you're downsampling the WGS experiment across entire genome, simple samtools view -s would do it. Just be careful with using different seeds each time if you're doing repetitive subsampling, otherwise each time would generate the exact same subsample.

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written by Vitis Vitis

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