SNP filtering

1

Hello everyone,

I am trying to filter .vcf files to contain only single point SNP and remove indel.

I have remove indel from the .vcf file by using the following command:

grep -v $'t-t' in.vcf > no_indels.vcf

I am able to remove indel from .vcf file.

But I also want to remove any SNP corresponding to CAT --> C and C --> CTATGG

I just want my .vcf file to contain only A-T, or T-A or G-C.

I mean just one single point mutation only.

Can anyone please help me with this?


files


.vcf


SNP

• 274 views

Please don't use grep to do this. Use a reliable VCF parser instead.

bcftools view -v snps should do the trick.


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