Script:hisatgenotype genotyping samples

From HISAT-genotype
Jump to: navigation, search

The python script will analyze genomic regions of interest using reads that are extracted from using Please avoid directly running the script on whole genomic sequencing reads as we might experience an issue described here. A tutorials for the script can be found at HLA typing. The script is designed to analyze many samples.


Argument Description Default Example
--base Base file name for index, variants, haplotypes, etc. genotype_genome --base genotype_genome
--region-list Comma separated list of regions (empty) meaning every region available --region-list hla.A,hla.B,hla.C,codis.FGA,cyp.2D6
--read-dir Name of directory where read files are placed (empty) --read-dir test_input
--out-dir Output directory name (empty) --out-dir test_output
-f / --fasta Reads are provided in FASTA format false -f
--num-editdist Number of maximum edit distance or mismatches allowed in the alignment, typing, and assembly of a read (not a pair) 2 --num-editdist 0
-p / --threads Number of threads to be used 1 -p 4
--assembly Perform assembly of each locus of interest disabled --assembly
--verbose Provide more information disabled --verbose
-h / --help Output help message disabled --help


 $ -p 4 --region-list hla --read-dir test_input --out-dir test_output