GATK 变异分析对于大数据样本可能会比较慢，因此可以按照染色体拆分后进行多线程并行计算。下面是我写的一个python多线程脚本，仅供参考，拙劣之处敬请指正。

#!/usr/bin/python3

import _thread
import os

import threading
import time

muthreads=[]
bam_file="a.mkdup.bam"
out_file_prefix="flower" 
chr_list=["CHR01","CHR02","CHR03","CHR04","CHR05","CHR06","CHR07","CHR08","CHR09","CHR10","CHR11","CHR12","CHR13"]
for chr in chr_list:

    threads_comonder_name= "gatk   HaplotypeCaller --intervals " + chr +"  -R /mnt/j/BSA/02-read-align/Tifrunner2.fasta -I " + bam_file + "   -ERC GVCF -O "+ out_file_prefix +"-"+chr+".erc.g.vcf"
    muthreads.append(threads_comonder_name)

exitFlag = 0

class myThread (threading.Thread):
    def __init__(self, threadID, name, counter, comander):
        threading.Thread.__init__(self)
        self.threadID = threadID
        self.name = name
        self.counter = counter
        self.comander = comander
    def run(self):
        print ("开始线程：" + self.name)
        print_time(self.name, self.counter, 5, self.comander)
        print ("退出线程：" + self.name)

def print_time(threadName, delay, counter,comander):
          # while counter:
   if exitFlag:
      threadName.exit()
   time.sleep(delay)

   print(comander)
   os.system(comander)#调用操作系统命令行处理数据
        # counter -= 1
# 创建新线程
threadlist=[]
for i, threadsnu in enumerate(muthreads[0:11]):
    print(i)
    print(threadsnu)
    threadsnew=myThread(1, "Thread-" + str(i), 2, threadsnu)
    threadlist.append(threadsnew)
# 开启新线程
for threads in threadlist:
    threads.start()
for threads in threadlist:
    threads.join()

print ("运行结束退出主线程")

下面的来自网络未验证

多条染色体的同样本的vcf文件合并

# for i in {1..22} X Y ;do echo "-I final_chr$i.vcf" '\';done
# for i in {10..19} {1..9} M X Y ;do echo "-I final_chr$i.vcf" '\';done
module load java/1.8.0_91
GATK=/home/jianmingzeng/biosoft/GATK/gatk-4.0.3.0/gatk
$GATK GatherVcfs  \
-I final_chr1.vcf \
-I final_chr2.vcf \
-I final_chr3.vcf \
-I final_chr4.vcf \
-I final_chr5.vcf \
-I final_chr6.vcf \
-I final_chr7.vcf \
-I final_chr8.vcf \
-I final_chr9.vcf \
-I final_chr10.vcf \
-I final_chr11.vcf \
-I final_chr12.vcf \
-I final_chr13.vcf \
-I final_chr14.vcf \
-I final_chr15.vcf \
-I final_chr16.vcf \
-I final_chr17.vcf \
-I final_chr18.vcf \
-I final_chr19.vcf \
-I final_chr20.vcf \
-I final_chr21.vcf \
-I final_chr22.vcf \
-I final_chrX.vcf \
-I final_chrY.vcf \
-O merge.vcf 
合并的时候需要注意，vcf文件的顺序跟每个vcf文件里面头文件顺序是相同的。