Thread: SNP filtering
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Old 07-22-2021, 11:56 AM   #1
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Location: dallas

Join Date: Jul 2021
Posts: 1
Default SNP filtering

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?
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