Hello,
[farukge@bio-hpc05 data]$ grep "1 15926506" dbsnp_138.b37.vcf
1 15926506 rs373703898 ATC A . . RS=373703898;RSPOS=15926507;d bSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000001000002000200;WGT=1;VC=DIV;OTHERKG
1 15926506 rs374926831 ATT A,AT . . RS=374926831;RSPOS=15926508;d bSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000001000002000210;WGT=1;VC=DIV;OTHERKG;NOC
1 159265062 rs2427824 T C . . RS=2427824;RSPOS=159265062;db SNPBuildID=100;SSR=0;SAO=0;VP=0x05012808000115051f000100;WGT=1;VC=SNV;PM;PMC;SLO;INT;VLD;G5;HD;GNO;KG Phase1;KGPilot123;KGPROD;OTHERKG;PH3;CAF=[0.1915,0.8085];COMMON=1
When I try to merge two vcf, i get error since ref is different for same position. How can I fix this? There are tons of this I assume, fixing a few wont be a solution.
[farukge@bio-hpc05 data]$ grep "1 15926506" dbsnp_138.b37.vcf
1 15926506 rs373703898 ATC A . . RS=373703898;RSPOS=15926507;d bSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000001000002000200;WGT=1;VC=DIV;OTHERKG
1 15926506 rs374926831 ATT A,AT . . RS=374926831;RSPOS=15926508;d bSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000001000002000210;WGT=1;VC=DIV;OTHERKG;NOC
1 159265062 rs2427824 T C . . RS=2427824;RSPOS=159265062;db SNPBuildID=100;SSR=0;SAO=0;VP=0x05012808000115051f000100;WGT=1;VC=SNV;PM;PMC;SLO;INT;VLD;G5;HD;GNO;KG Phase1;KGPilot123;KGPROD;OTHERKG;PH3;CAF=[0.1915,0.8085];COMMON=1
When I try to merge two vcf, i get error since ref is different for same position. How can I fix this? There are tons of this I assume, fixing a few wont be a solution.
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