genotype-snps

Given the normal BAM file, this step of HATCHet identifies heterozygous germline SNP positions. The user can restrict candidate positions to a given list (e.g., dbSNP) using the -R, --snps argument.

Input

genotype-snps takes in input a sorted and index BAM file from a matched-normal sample and an indexed human reference genome (preferrably the same version as was used for alignment).

Name	Description	Usage
-N, --normal	A sorted-indexed BAM file	The matched normal sample
-r, --reference	A FASTA file	The human reference genome used for germline variant calling

Output

genotype-snps produces a tab-separated VCF file for each chromosome which contains a list of the genomic positions that have been identified as germline heterozygous SNPs in the matched-normal sample.

Name	Description	Format
-l, --outputsnps	the output file for the list of identified heterozygous germline SNPs	#CHR POS

Main parameters

Name	Description	Usage	Default
-R, --snps	VCF files	Optional list of candidate SNP positions to consider	None*
-st, --samtools	Path to bin directory of SAMtools	The path to this direcoty needs to be specified when it is not included in $PATH	Path is expected in the enviroment variable $PATH
-bt, --bcftools	Path to bin directory of BCFtools	The path to this direcoty needs to be specified when it is not included in $PATH	Path is expected in the enviroment variable $PATH
-c, --mincov	Minimum coverage	Minimum number of reads that have to cover a variant to be called, the value can be increased when considering a dataset with high depth (>60x)	0
-C, --maxcov	Maximum coverage	Maximum number of reads that have to cover a variant to be called, the typically suggested value should be twice higher than expected coverage to avoid sequencing and mapping artifacts	1000
-j, --processes	Number of parallel jobs	Parallel jobs are used to consider the chromosomes in different samples on parallel. The higher the number the better the running time	2

*When run as a standalone module, the no SNP list is used by default. When run as part of hatchet run and no --snps argument is supplied, the correct version of dbSNP is automatically downloaded and used to call SNPs.

Optional parameters

Name	Description	Usage	Default
-v, --verbose	Verbose logging flag	When enabled, count-alleles outputs a verbose log of the executiong	Not used
-q, --readquality	Threshold for phred-score quality of sequencing reads	The value can be either decreased (e.g. 10) or increased (e.g. 30) to adjust the filtering of sequencing reads	0
-Q, --basequality	Threshold for phred-score quality of sequenced nucleotide bases	The value can be either decreased (e.g. 10) or increased (e.g. 30) to adjust the filtering of sequenced nucleotide bases	11
-E,--newbaq	Flag to enable newbaq veafute of SAMtools	When selected, the user asks SAMtools to recompute alignment of reads on the fly during SNP calling	Not used