10XGenomics / vartrix

Single-Cell Genotyping Tool
MIT License
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error of vcf format #67

Open songeric1107 opened 2 years ago

songeric1107 commented 2 years ago

keep getting the errors as:

Vartrix error. v1.1.22. Error: failed to open BCF/VCF from "genome1K.phase3.SNP_AF5e2.chr1toX.hg38.mod2.vcf"

the vcf file looks like the following:

CHROM POS ID REF ALT QUAL FILTER INFO

chr1 11008 rs575272151 C G 100 PASS AF=0.0880591 chr1 11012 rs544419019 C G 100 PASS AF=0.0880591 chr1 13116 rs62635286 T G 100 PASS AF=0.0970447 chr1 13118 rs200579949 A G 100 PASS AF=0.0970447 chr1 13273 rs531730856 G C 100 PASS AF=0.0950479 chr1 14464 rs546169444 A T 100 PASS AF=0.0958466 chr1 14599 rs531646671 T A 100 PASS AF=0.147564 chr1 14604 rs541940975 A G 100 PASS AF=0.147564 chr1 14930 rs75454623 A G 100 PASS AF=0.482228 chr1 15211 rs78601809 T G 100 PASS AF=0.609026 chr1 15274 rs62636497 A G,T 100 PASS AF=0.347244,0.640974 chr1 15820 rs2691315 G T 100 PASS AF=0.410543 chr1 18849 rs533090414 C G 100 PASS AF=0.951877 chr1 30923 rs806731 G T 100 PASS AF=0.872404 chr1 49298 rs200943160 T C 100 PASS AF=0.782149 chr1 49554 rs539322794 A G 100 PASS AF=0.063099 chr1 51479 rs116400033 T A 100 PASS AF=0.128195 chr1 52238 rs2691277 T G 100 PASS AF=0.921725 chr1 54490 rs141149254 G A 100 PASS AF=0.0960463 chr1 54716 rs569128616 C T 100 PASS AF=0.289137 chr1 55164 rs3091274 C A 100 PASS AF=0.923323 chr1 55545 rs28396308 C T 100 PASS AF=0.239217 chr1 58814 rs114420996 G A 100 PASS AF=0.109026 chr1 59040 rs62637815 T C 100 PASS AF=0.0615016 chr1 60351 rs62637817 A G 100 PASS AF=0.0549121 chr1 62777 rs528401309 A T 100 PASS AF=0.25639 chr1 63268 rs75478250 T C 100 PASS AF=0.353035 chr1 63671 rs80011619 G A 100 PASS AF=0.1875

Cathy94 commented 1 year ago

Hello, I also met the problem, could you tell me how to solve this? Thank you!