Merge VCF 的方法：

1. gatk mergVcf

gatk MergeVcfs -I M11189W.chr21.common.g.vcf.gz -I N11189.chr21.common.g.vcf.gz -O merged.picard.vcf.gz

Error: has sample entries that don't match the other files.

参考GATK mergevcf模块，注意两个vcf要相互match

2. gatk GatherVcfs

gatk GatherVcfs I=35.vcf I=36.vcf O=all.vcf

3. bcftools

bcftools merge --merge all file1.vcf.gz file2.vcf.gz -O v -o merged.vcf.gz

4. python: bioinfokit package

from bioinfokit.analys import marker

# concatenate VCF files. You can provide multiple VCF files separated by comma.

marker.concatvcf("file_1.vcf,file_2.vcf,file_3.vcf,file_4.vcf")# merged VCF files will be stored in same directory (concat_vcf.vcf)

5. snpsift

java -jar SnpSift.jar split -j *.vcf > combined.vcf