Remove duplicates

Question

[am29]

Is there some easy way to remove duplicates from the vcf file? I just want to get rid of the list of duplicated SNPs, not to leave one of the duplicates, but to delete them all. I already tried with bcftools but it didn't work. Now, I am trying to delete them using --exclude intervals from GATK, but I would like to find some other solution if possible. Is there some quick way to just delete lines/SNPs from vcf file?

Answer 1

[Pierre Lindenbaum]

a java code:

compile:

wget -O picard.jar "https://github.com/broadinstitute/picard/releases/download/2.26.8/picard.jar"
javac -cp picard.jar Biostar9502101.java

execute:

cat in.vcf | java -cp picard.jar:. Biostar9502101

[am29]

Thank you, this worked!

Answer 2

[ATpoint]

how can i remove duplicated variants from vcf file?

how to remove duplicate SNP rows in vcf using bcftools norm

[am29]

Thanks for the quick answer, but I have already seen those and that's not what I need. I want to delete not only the duplicate but the "nonduplicate" too. So, if there is SNP1 4356789 and SNP1 4356789 I want to get rid of both. Not to leave one of them, but to delete both.