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any tutorials for structural variants filtering and prioritization

Outputs from structural variants callers like breakdancer, lumpy and delly contains false positives.

How do you filter out those false positives and then prioritize the SVs? Anyone has a good resources or experiences on that ?

Thanks!

structural-variants dna-sequencing
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updated by Ram Ram • written by Ming Tommy Tang Ming Tommy Tang

Thanks Heng for your reply! I happen to read this post before. I am wondering have you written any tutorials for that?

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written by Ming Tommy Tang Ming Tommy Tang

1 answer

Any idea how you would filter predictions from breakdancer?

One simple way is filter the output based on prediction score and read counts

# $9= prediction score
# $10= supporting reads

cat libraryP1.ctx | awk 'BEGIN {OFS="\t"} { if ($9 >= 40 && $10 >= 5) { print $0 }}' | wc -l
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updated by Ram Ram • written by Chirag Nepal Chirag Nepal

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