Applied Genomics Coding

mkdir DirName

Make a new directory

cd DirName

Change directory to the DirName directory that is within the current folder

cd ~

Return to login directory

cd ..

Change directory to the next one above this one

pwd

Show the path for the directory that I’m in now

ls

Show the files in the current directory

cp

Copy a file (e.g. cp oldname.txt newname.txt

cat

Show the contents of a file (e.g. cat filename.txt)

rm

Delete (e.g. rm filename.txt)

mv

Rename a file (e.g. oldname.txt newname.txt)

head

Show the first 10 lines of a file (ex. head - x = first x lines)

tail

Show the last 10 lines of a file

grep

Search inside the files for an item (e.g. grep blue *.txt or for the number 5: grep -n 5 file name)

sort

Sort a file on a column number (-k N for column N, -g for number sort) (e.g. sort -g -k 1 file name)

man commandname

Prints out the entry from the user manual for that command

nedit

Open a text editor in a new window

xterm

Spawn a new command window

Get back to directory

cd directory name/

ls -lh file name

Gives the size of a file

wc -l file name

Gives the number of lines in the file

head -n file name > new file name

Captures the first n lines of a file

cp /shared/files/file name .

copy files to the home directory

gz file name

unzips a file (gz files are zipped)

bwa index file name

Ensure a file is used efficiently by BWA

.sam file

reports the read sequence, the read quality, and where it maps to on the genome

Sam format vs Bam format

Sam format = human readable whereas bam format = machine readable

navigating tview

• Hit letter g and then enter =position and it will take you to that position

• Y = heterozygous

Identifying a file needs to be indexed

• If asked to sort a file and then given this command: samtools tview ERR495003-pe-sorted.bam GCF_000195835.2_ASM19583v2_genomic.fna

• You would need to identify that the file needs to be sorted and sort it by indexing it - samtools index ERR495003-pe-sorted.bam

.vcf file

The first few lines will inform you on how to read the outputs

Capture the numbers from the second column of a file for the last 3096 columns (to cut out the header)

gawk ‘{print $2}’ ERR495003.vcf | tail -n 3096 > ERR495003.pos

PLINK

Two basic file types in PLINK

• .ped

• .map = tell you where things are

• Sex is typically coded as 1 (male), 2 (female), or 0 (unknown)

• Phenotypes are typically coded for case-control analyses as 2 (affected), 1 (unaffected), or -9 (unknown)

• Genotypes can be coded in a range of ways, but typically alleles are coded as paired combinations of A, C, G, T, or 0

pink --file file name --freq --out file name

Allele frequencies for .ped and .map files

plink --file file name --het --out file name

--het command computes observed and expected homozygous genotype counts for each sample and reports F coefficients

plink --bfile test --genome --cluster --out test

• --genome → calculate pairwise IBD/relatedness between individuals

• --cluster → perform clustering based on the genetic relationships

cat Test.genome | grep Fam1..64 | grep 0.5 | wc -l

This command is essentially counting how many rows in Test.genome match individual 64 and have a value of 0.5 somewhere in the row.