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。
以上就是python实现GATK多线程加速示例的详细内容，更多关于python GATK多线程加速的资料请关注Devmax其它相关文章！