variant filtering based on high quality reference - removing false positives

Question

[nobody]

Hello Wonderful people !!!

I'm new to the world of bio-informatics and this is my first post, so please forgive me for any unintended mistake ...

The VCF file that I'm working on are missing ##INFO variables like QD, FS, SOR, MQ, MQRankSum, ReadPosRankSUm, InbreedingCoeff ... may be one can generate them first and then do the variant quality control ...

but at this stage I just want to do some basic quality control on the variants in my VCF files ...

https://www.nist.gov/programs-projects/genome-bottle provides the high quality reference for variants calling ...

Is there a way by which I can select only the variants that are present in the reference VCF file?

I have used bcftools till now for normalization and to filter out samples from VCF file ..

may anyone please direct me on how to achieve the above task ? This help would be much appreciated ...

thanks team ...

Answer 1

[4galaxy77]

Download the high quality reference and then print out all the SNPs.

bcftools view -v snps reference.vcf | bcftools query -f'%CHROM\t%POS\n'  > reference_positions.txt

Then extract these positions from the target vcf.

bcftools view -T reference_positions.txt target.vcf > target_filtered.vcf

If you also want to include indels, then you can add it into the -v argument under bcftools view on the first line.

Answer 2

[nobody]

@4galaxy77 oh my wonderful friend ... much love and respect to you !!! may the force be with you ... forever and ever !!! I will try this approach and revert back if any further question .... much thanks !!!