Retrieving information from FASTA file

Question

[Maryam]

Hello,

I have been working with tumour sample sequencing data. All I need to do is to open the VCF and Bam files in IGV and retrieve the variant information but it is really time consuming to look for every variant in large number of sample FASTA file and manually type in the data sheet. I wanted to ask can we extract our desirable information from Bam and VCF files using R programming? If yes then can someone guide me how to do that?

Thank you!

[Pierre Lindenbaum]

but it is really time consuming to look for every variant in large number of sample FASTA file and manually type in the data sheet.

what does that mean ? what information are you looking for ?

[Maryam]

I want to check the DP, QUAL, AF for my set if variants from VCF file. Also from BAM file I check the number of reads for ref allele as well as alt allele and the % of my alt allele. I do this for each and every mutation by looking into the VCF and Bam file. I need an easy way.

Thank you!

[Pierre Lindenbaum]

so your question is not at all related to a FASTA file.

I want to check the DP, QUAL, AF for my set if variants from VCF file.

use bcftools query

Also from BAM file I check the number of reads for ref allele as well as alt allele and the % of my alt allele.

look at the FORMAT/AD field in your VCF.