mdsumner

docker pull ghcr.io/rocker-org/verse:4.3.3
docker run --rm -ti ghcr.io/rocker-org/verse:4.3.3  bash
 
quarto create project book abook

cd abook
## I turned off PDF rendering in _quarto.yml because lots of deps
quarto render

elowy01

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

adefelicibus

Install Samtools, BCFTools and htslib on linux

Install some build dependencies

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev

[samtools]

wojteklu

Code is clean if it can be understood easily – by everyone on the team. Clean code can be read and enhanced by a developer other than its original author. With understandability comes readability, changeability, extensibility and maintainability.

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General rules

1. Follow standard conventions.
2. Keep it simple stupid. Simpler is always better. Reduce complexity as much as possible.
3. Boy scout rule. Leave the campground cleaner than you found it.
4. Always find root cause. Always look for the root cause of a problem.

Design rules

rich-iannone

# Create a simple data frame for testing
df <- data.frame(POSIXtime = seq(as.POSIXct('2013-08-02 12:00'),
                             as.POSIXct('2013-08-06 05:00'), len = 45),
                 x = seq(45))

# The Subset Examples
#
# All data on 2013-08-06
sub.1 <- subset(df, format(POSIXtime,'%d')=='06')