Hello, I have a variants result of mtDNA sequencing. Here is my result like:
SampleID Pos Ref Variant Major/Minor Variant-Level Coverage-FWD Coverage-Rev Coverage-Total R07058.bam 9090 T C C/A 0.9974 2100 2136 4236
This result comes from mtDNA-Server. Major means major nucleotide at 1 site, minor means opposite. Variant-Level seems to mean the ratio of variants, but I am not sure about that.
I want to annotate those variants by using snpEff which needs input VCF file, so I try to write a python script to convert this to VCF format file. I already read VCF format required before I started.
Considering that mitochondrial is haploid I separate each variant of same site as different variants in VCF. In this example it would be 2 lines in VCF:
#CHROM POS ID REF ALT ... MT 9090 . T A ... MT 9090 . T C ...
I hope this solution is right.
My questions is about INFO columns in VCF. mtDNA is haploid however it may have many(unknow) copies in cell, I don't know how to fill this tag in INFO:
- AC : allele count in genotypes, for each ALT allele, in the same order as listed.
- AN : total number of alleles in called genotypes.
- DP : combined depth across samples, e.g. DP=154. I know it would be many depth values because more than 1 sample will be put in 1 line in VCF. But I don't know what is combined depth across them and how to calculate.
Any help is appreciate.