User: panbar

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panbar20
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I am new in to Cancer Bioinformatics 

Posts by panbar

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Answer: A: minor allele frequency (MAF) from vcf
... It is easy to do with awk. I found an easy way as follows. for single input snv vcf file awk '$1=="#CHROM" {print $0 "\tMAF"; next}; NF { info=$8; gsub(/.*;DP4=|;MQ=.*/, "", info); split(info, a, /,/); print $0 "\t" (a[3]+a[4])/(a[1]+a[2]+a[3]+a[4])}' inputfile.vcf > outputfile.vcf for ...
written 4.0 years ago by panbar20
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COmparing two SNV vcf files using bedtools
... I have two SNV vcf files A.vcf and B.vcf I would like to find the - common SNVs between A and B - SNVs unique for A - SNVs unique for B I tried bedtools intersect option for finding common between A and B. > bedtools intersect -a A.vcf -b B.vcf > ABcommon.vcf Can anyone suggest how to ...
vcf bedtools intersect written 4.0 years ago by panbar20 • updated 4.0 years ago by jasper191810
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minor allele frequency (MAF) from vcf
... How minor allele frequency (MAF) is calculated from the DP4 fields of vcf file? Can anyone help with a unix shell script? ...
genome next-gen snp sequencing written 4.2 years ago by panbar20

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