gatk pipeline based on python

---

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:

 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!
--------------------------------------------------------------------

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