001. Test data
[root@PC1 test]# ls ## test data seg1_1.vcf seg1_2.vcf seg1_3.vcf [root@PC1 test]# ll - h total 1 .2G -rw-r--r--. 1 root root 392M Dec 1 18 : 14 seg1_1.vcf -rw-r--r--. 1 root root 410M Dec 1 18 : 15 seg1_2.vcf -rw -r--r--. 1 root root 386M Dec 1 18 : 14 seg1_3.vcf
002. Merge vcf files
g atk MergeVcfs -I seg1_1.vcf -I seg1_2.vcf -I seg1_3.vcf -O xxx.vcf ## merge command
The combined result is as follows:
[root@PC1 test]# ls seg1_1.vcf seg1_2.vcf seg1_3.vcf xxx.vcf xxx.vcf.idx [root@PC1 test]# ll - h total 2 .4G -rw-r--r--. 1 root root 392M Dec 1 18 : 14 seg1_1.vcf -rw-r--r--. 1 root root 410M Dec 1 18 : 15 seg1_2.vcf -rw-r--r--. 1 root root 386M Dec 1 18 : 14 seg1_3.vcf -rw-r--r--. 1 root root 1 .2G Dec 1 19 : 16 xxx.vcf -rw-r--r--. 1 root root 6.2K Dec 1 19 : 16 xxx.vcf.idx
003. Generate a list of vcf files that need to be merged
[root@PC1 test]# ls seg1_1.vcf seg1_2.vcf seg1_3.vcf vcf.list [root@PC1 test]# cat vcf.list ## Vcf list file to be merged seg1_1.vcf seg1_2.vcf seg1_3.vcf [root@PC1 test]# java -jar /home/software/picard/picard.jar MergeVcfs I=vcf.list O=xxx.vcf ## merge command
004. Merge result
[root@PC1 test]# ls seg1_1.vcf seg1_2.vcf seg1_3.vcf vcf.list xxx.vcf xxx.vcf.idx [root@PC1 test]# ll - h total 2 .4G -rw-r--r--. 1 root root 392M Dec 1 18 : 14 seg1_1.vcf -rw-r--r--. 1 root root 410M Dec 1 18 : 15 seg1_2.vcf -rw-r--r--. 1 root root 386M Dec 1 18 : 14 seg1_3.vcf -rw-r--r--. 1 root root 33 Dec 1 19 : 24 vcf .list -rw-r--r--. 1 root root 1.2G Dec 1 19 : 24 xxx.vcf -rw-r--r--. 1 root root 6 .2K Dec 1 19 : 24 xxx.vcf.idx
