Bioinformatics Tools
GitBook allows you to organize your book into chapters, each chapter is stored in a separate file like this one.
Samtools
Samtools is a suite of programs for analyzing large scale sequencing data. It contains three separate packages samtools, BCFtools, and HTSlib.
Samtools documentation can be found here.
Examples:
Selected regions of bam file and output to another bam file.
samtools view aln.sorted.bam chr2:20,100,000-20,200,000 -b > out.bam
Select regions from fastq file
samtools faidx teo20.fa 1:1-10000
Kmer Approaches
Pan Kmer reference, see Dolle et al., BioRxiv
Imputation
Rapid genotype imputation from seq without ref panels. Davies, et al., 2016.