diff --git a/docs/methylextraction.md b/docs/methylextraction.md index 3c2adc9..dd96c77 100644 --- a/docs/methylextraction.md +++ b/docs/methylextraction.md @@ -13,6 +13,9 @@ file: ```bash $ biscuit vcf2bed -t cg my_pileup.vcf.gz > my_pileup.bed ``` +For BISCUIT version 1.5.0 and earlier, the minimum coverage by default is 3. This setting was good for traditional WGBS; +however, for low input and single cell protocols, this option should be changed to 1 (`biscuit vcf2bed -k 1 ...`). +BISCUIT version 1.6.0 and later have the default value switched to 1 to avoid user confusion. The `-t` flag can be used to retrieve mutation and other information, including