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fix typo
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@tobiasrausch
tobiasrausch committed Jan 10, 2024
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Expand Up @@ -149,7 +149,7 @@ Read-depth profiles can also be segmented at the same time.

The segmentation is in VCF format but you can extract a BED-like file using bcftools.

`bcftools query -f "%CHROM\t%POS\t%INFO/END\t%ID\t[%RDCN]\n" cnv.bcf > segmentation.bed`
`bcftools query -f "%CHROM\t%POS\t%INFO/END\t%ID[\t%RDCN]\n" cnv.bcf > segmentation.bed`

Plotting:

Expand Down Expand Up @@ -208,7 +208,7 @@ Somatic copy-number alterations (SCNAs)

* Optional: Plot the SCNAs using bcftools and R.

`bcftools query -s tumor -f "%CHROM\t%POS\t%INFO/END\t%ID\t[%RDCN]\n" somatic.bcf > segmentation.bed`
`bcftools query -s tumor -f "%CHROM\t%POS\t%INFO/END\t%ID[\t%RDCN]\n" somatic.bcf > segmentation.bed`

`Rscript R/rd.R tumor.cov.gz segmentation.bed`

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