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Remove duplicates

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?

remove duplicates vcf
• 2,104 views • link
updated by robertperkins224 • robertperkins224 • written by am29 • am29

2 answers

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
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you, this worked!

• 0 views • link
written by am29 • 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.

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written by am29 • am29

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