Extraction of information from VCF file
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Thank you for providing this wonderful tool.
As a beginner, I am still struggling to comprehend the structure of the VCF file. I executed the following command:
./minipileup -vcC -a 1 -f /lab/user/ref_bioedit.fa /lab/user/bam_file.dedup.bam > var.vcf.
Now, I am wondering how to interpret the variants listed in the example:
Aga 928 . C A,G,T 161 . . GT:ADF:ADR 3/0:18,2,3,73:18,1,6,88.
I already know that the exact variant is (ref: C and alt: T).
- How can I filter out insignificant substitutions or insertions and display only the relevant ones?
- Additionally, how can I determine the number of reads supporting a variant per sample?
- final question is there a way to add a tag in order to know the type of variant ( snp , insertion , deletion ? )
@lh3 could you please help me with this !!!
I am afraid that you will have to write a script. You can also try bcftools but I am not sure if it can do the job for you.