I mapped raw reads obtained from an E. coli genome (.fastq file) to my reference genome. Next, I exported the .vcf (variant calling file), which looks something like the header example shown below (total >50 lines):
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Variants:_LGC19-XL01_S63_L001_R_001_(trimmed)
CFC381_K12_Bw25113 360287 . GGGAAT AATTCC 1952.76 . NS=1;VF=0.380;SB=0.533;SB50=0.60;SB65=1.0;TYPE=Substitution;AVQUAL=30 DP:AO 231:89
How can I back-fill or quickly assign the missing GTs to the .vcf
?
For my downstream process (plink --pca
, via bfctools merge
), I need that there are GT entries in every .vcf
, so I can merge them and the respective GT is shown in the merged .vcf
. I only found solutions that need the .bam
file, but that is laborious and I don't think I need the .bam
in the case of haploid data.
- This method needs
.bam
: https://www.biostars.org/p/319304/ - This method needs
.fastq
: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html#examining-the-results
However, the.fastq
is actually from a mixed culture, so I wonder do I really need to follow the .bam
-strategy? Suggestion for a tool? But in that case, why did it not export the GTs in the fist place (I exported from "geneious" sequence analysis program)