Thank you for always help. I have an additional problem.
I would like to merge two vcf files (a.vcf, b.vcf) into one vcf file (c.vcf) using GATK CombineVariants. a.vcf and b.vcf have have same variants but don't regard same variants. Specifically, a.vcf and b.vcf are shown as below;
$ cat a.vcf
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB chr1 897460 v5_202 A <*:DEL> . PASS . GT:AD:DP 0/0:20,0:20 0/1:14,14:28
$ cat b.vcf
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleC SampleD chr1 897459 v6_202 CA C 2068.83 PASS . GT:AD:DP 0/0:43,0:43 0/1:40,6:46
As you can see, these files have a data of same variant, but coordinates are different. I want to merge the two files into one file and merge these two variant data into one variant data using GATK CombineVariants.
How should I merge the files?