gatk calling variants include two mode, the first one is single calling (produce gvcf for each sample), the second one is population calling (directly produce vcf include all sample).
It also supports genome splitting by setting -ss or -sn, if you split the genome, it will calling variant on each split region.
specify the input directory by setting the -i parameter, It will automatically look for files ending with suffix_name (by setting the -S options)in this directory.
usage: gatk.py [-h] [-v] -i -o [-m] [-sn | -ss ] [--split-mode] [-hcjo] [-cgjo] [-ggjo] [-mvjo] [--gvcf] [-s [...]] [-p] [-pbi] [-t] -r [-n] [-l]
The purpose of this program is for calling snp used gatk!
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optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-i , --indir the directory where bam located
-o , --outdir the directory save the snp and indel calling result
-m , --mode the calling mode, pc: population calling, sc: single calling [sc]
-sn , --split-num the number of split genome
-ss , --split-size the size for split genome [unit M]
--split-mode the mode of split genome [imprecise]
-hcjo , --haplotypecaller-java-options
the java options for HaplotypeCaller, such as -Xmx100G limit the memory usage
-cgjo , --combinegvcf-java-options
the java options for CombineGVCFs
-ggjo , --genotypegvcf-java-options
the java options for GenotypeGVCFs
-mvjo , --mergevcf-java-options
the java options for MergeVcfs
--gvcf output gvcf file , default output is vcf file [False]
-s [ ...], --suffix-name [ ...]
the suffix name of input file [default sort.fixmate.rmdup.bam]
-p , --process the porcess number for deal with multiple samples [5]
-pbi , --process-build-index
the process of build bam index [5]
-t , --threads the threads for index and sort bam file [5]
-r , --ref the reference genome
-n , --prefix-name the prefix name of output vcf file [All]
-l , --log the log file for record running information [gatk.log]
For command line option of each command, type: gatk.py COMMAND -h