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Removing sites/reads from BGZIp VCf

I have a vcf compressed and indexed (.vcf.gz and .tbi)

I have a list of sites that I need to remove from this file (delete forever) while having the other information.

Eg:

chr8 pos:125907085:125907085

what would be the best way to go about this?

vcf tabix filter
• 2,640 views • link
updated by Ram Ram • written by ali • ali

1 answer 

gunzip -c file.vcf.gz |\
awk -F '\t' '!($1=="chr8" && int($2)==125907085))' > out.vcf && \
bgzip out.vcf && \
tabix -p vcf out.vcf.gz
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

is there a more optimal way of achieving this, lets say i have like 100 positions to remove

eg:

chr1 start-end

chr8 start-end

• 0 views • link
written by ali • ali

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