Extraction of information from VCF file

QuentinPerriere commented 3 months ago

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 ? )

QuentinPerriere commented 3 months ago

@lh3 could you please help me with this !!!

lh3 commented 2 months ago

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.

lh3 / minipileup

Extraction of information from VCF file #7