GATK tool to merge INDEL with SNPs with the same set of samples
Hi All,
I am trying to merge two VCF files, one with SNPs and the other with INDELS. I was looking at these three methods, but I am not quite clear on which one would be the right option for me. It is likely that these two VCFs have overlapping sites, so I am not sure if Picard would be the right tool. Could someone please help me figure out the right tool.
Option 1.
java -jar picard.jar MergeVcfs I=SNPs.vcf.gz I=INDELS.vcf.gz O=WXS_INDELS_SNPs.vcf.gz
Option 2.
${JAVA} ${JAVAOPTS} -jar ${GATK} GatherVcfs -I SNPs.vcf.gz -I INDELS.vcf.gz -O WXS_INDELS_SNPs.vcf.gz
Option 3
bcftools merge --merge all SNPs.vcf.gz INDELS.vcf.gz --force-samples -O z -o WXS_INDELS_SNPs.vcf.gz
PS. I just checked these three methods. I found the results from Option 1 and Option 3 are the same, and GatherVcfs is not suitable for this kind of merge.
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Hi,
BCFtools works just fine-
Merging and concatenation are two different operations. I am assuming since you have same sets of samples in the VCFs and you are trying to join them together, you mean concatenation rather than merging (correct my if I am wrong). Concatenation is vertical joining whereas merging is horizontal joining. GatherVCFs is concatenating whereas other options are merging.