Script:hisatgenotype genotyping samples

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hisatgenotype_genotyping_samples.py

The hisatgenotype_genotyping_samples.py python script will analyze genomic regions of interest using reads that are extracted from using hisatgenotype_extract_reads.py. 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.

Arguments:

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

Examples:

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