Question: VCF Merge using Vcf Tools
0
ankur.c • 0 wrote:
Hello,
I tried combining two vcf files using vcf tools merge. The problem I am facing is that the tool is adding the depth of the two vcf files when I dont want to do that and instead simply want it to take the higher of the two depths.
Command used;
bgzip file1.vcf
bgzip file2.vcf
tabix file1.vcf.gz
tabix file2.vcf.gz
vcf-tools merge file1.vcf.gz file2.vcf.gz > combined.vcf
Examples:
Combined.vcf:
chr7 295683 rs36173688 T TG 623.23 PASS AC=4;AF=1.00;AN=4;DB;**DP=37**;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;MQ=60.00;QD=30.62;RPA=4,5;RU=G;SF=0,1;SOR=5.994;STR GT:GQ:DP:PL:AD 1/1:57:19:619,57,0:0,19 1/1:54:18:702,54,0:0,18
File 1:
chr7 295683 rs36173688 T TG 581.73 PASS AC=2;AF=1.00;AN=2;DB;**DP=19**;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.62;RPA=4,5;RU=G;SOR=5.994;STR GT:AD:DP:GQ:PL 1/1:0,19:19:57:619,57,0
File 2:
chr7 295683 rs36173688 T TG 664.73 PASS AC=2;AF=1.00;AN=2;DB;**DP=18**;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.24;RPA=4,5;RU=G;SOR=5.892;STR GT:AD:DP:GQ:PL 1/1:0,18:18:54:702,54,0
As seen in the example with DP column in combined vcf has simply added the values from both of them when it shouldnt since its from the same patient data and I only want to merge the vcf files from different variant callers.