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filtering and statistics of depth per genotype per SNP of VCF files (solved)

Hello

I need to get the statistics of VCF file. I would like to see the distribution of read depth for each sample at each SNP.

I would like also to filter by this depth, sey, set the data point to NULL when the value is below a threshold.

Thank you

Hanan

snp next-gen
• 5,729 views • link
updated by Ram Ram • written by Hans Hans

Thank you for your response

I have used Bioconductor - VariantAnnotation R package so I can easily manipulate the statistics.

read vcf file with obj<-readVcf( ) and look at the obj@assays$data@listData[["DP"] matrix.

Hanan

• 1 views • link
updated by Ram Ram • written by Hans Hans

2 answers

If your VCF contains the DEPTH (DP) information in the FORMAT section. Use awk to get the index of this DP-column and extract the DP for each sample:

$ curl -sL "https://raw.githubusercontent.com/chmille4/ngs_server/89f038f986747390d190baf09efa93a8897c0ec6/ext/vcftools/examples/valid-4.1.vcf" |\
awk -F '     ' '/^#CHROM/ {split($0,samples);next;} /^#/ {next;} {dpcol=-1;n=split($9,fmt,/\:/);for(i=1;i<=n;++i) if(fmt[i]=="DP") { dpcol=i;break;} if(dpcol==-1) next; for(i=10;i<=NF;++i) {split($i,a,/\:/);printf("%s\t%s\t%s\t%s\n",$1,$2,samples[i],a[dpcol]);}}'
19    14370    NA00001    1
19    14370    NA00002    8
19    14370    NA00003    5
20    17330    NA00001    3
20    17330    NA00002    5
20    17330    NA00003    3
20    1110696    NA00001    6
20    1110696    NA00002    0
20    1110696    NA00003    4
20    1230237    NA00001    7

(...)
• 1 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thank you, where do I put my local file name

• 1 views • link
updated by Ram Ram • written by Hans Hans

You can use vcftools

• 1 views • link
updated by Ram Ram • written by jesse.hoff • jesse.hoff

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