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Count of Indels and Point mutations

Hello Everyone,

Can anyone please tell me a way to count the Indels > 3 bp, Indels b/w 1 & 3 bp and also how to count the point mutations?

Thank you

vcf
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Vasu Vasu

are you able to develop a script in R?

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written by noeD noeD

I guess its easier to go with linux commands right

• 0 views • link
written by Vasu Vasu

1 answer

Indels > 3 bp

using vcffilterjs https://github.com/lindenb/jvarkit/wiki/VCFFilterJS

$ curl -s "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" | gunzip -c |   java -jar dist/vcffilterjs.jar -e 'function accept(v) {var alts=v.getAlternateAlleles(),refLen=v.getReference().length();for(var i=0;i<alts.size();++i) {var="" alt="alts.get(i);" if(alt.isSymbolic())="" continue;="" var="" altLen="alt.length();" if(="" Math.abs(refLen-altLen)="">=3) return true; } return false;}accept(variant);' | wc -l
15574

Indels b/w 1 & 3

curl -s "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" | gunzip -c |  java -jar dist/vcffilterjs.jar -e 'function accept(v) {var alts=v.getAlternateAlleles(),refLen=v.getReference().length();for(var i=0;i<alts.size();++i) {var="" alt="alts.get(i);" if(alt.isSymbolic())="" continue;="" var="" altLen="alt.length();" var="" diff="Math.abs(refLen-altLen);if(diff">1 && diff <3) return true; } return false;}accept(variant);' | wc -l
7388

point mutations? 

$ curl -s "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" | gunzip -c |  java -jar dist/vcffilterjs.jar -e 'variant.isSNP()' | wc -l
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks a lot. But I need small information. I don't have a vcf file. I'm using a mutation file from TCGA. Will it be same for this one too?

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written by Vasu Vasu

there is also an error

[main] ERROR jvarkit - <eval>:1:121 Expected ident but found = function accept(v) {var alts=v.getAlternateAlleles(),refLen=v.getReference().length();for(var i=0;i<alts.size();++i) {var="" alt="alts.get(i);" if(alt.issymbolic())="" continue;="" var="" altlen="alt.length();" if(="" math.abs(reflen-altlen)="">=3) return true; } return false;}accept(variant); ^ in <eval> at line number 1 at column number 121 [main] ERROR jvarkit - Command initialization failed 0

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written by Vasu Vasu

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