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To remove genotype "./." from vcf file with awk

Hi,

I need help with awk commands, I have 4 samples in my vcf files, so field $10,$11,$12,$13 are the fields which have the genotype for each row, now I want remove the rows where in any of the any rows at least one sample is showing the genotype ./. and want to print the rest in another vcf file, can this be done? Am not so familiar with awk substr. Any assistance? Below is the example of my vcf file, it does not have any header.

chr3    75787186    rs150410646    C    T    53.89    .    AC=4;AF=0.500;AN=8;BaseQRankSum=-4.341;DB;DP=424;Dels=0.00;FS=0.000;HaplotypeScore=2.2684;MLEAC=4;MLEAF=0.500;MQ=6.41;MQ0=371;MQRankSum=-3.553;QD=0.13;ReadPosRankSum=-1.007    GT:AD:DP:GQ:PL    0/1:63,21:80:48:48,0,127    0/1:25,5:29:21:21,0,64    0/1:142,41:174:10:10,0,94    0/1:95,31:120:6:6,0,120
chr3    75787576    rs141348932    A    G    61.87    .    AC=2;AF=1.00;AN=2;DB;DP=195;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=4.17;MQ0=189;QD=0.69    GT:AD:DP:GQ:PL    ./.    ./.    1/1:68,22:86:9:87,9,0    ./.
chr3    75787583    rs144348996    A    G    100.62    .    AC=2;AF=1.00;AN=2;DB;DP=203;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=4.33;MQ0=197;QD=1.12    GT:AD:DP:GQ:PL    ./.    ./.    1/1:65,25:86:12:126,12,0    ./.
chr3    75787584    rs151027881    C    A    93.62    .    AC=2;AF=1.00;AN=2;DB;DP=203;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=4.33;MQ0=197;QD=1.04    GT:AD:DP:GQ:PL    ./.    ./.    1/1:64,26:86:12:119,12,0    ./.
chr3    75787620    rs145606249    T    C    153.42    .    AC=2;AF=1.00;AN=2;DB;DP=224;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=4.38;MQ0=217;QD=1.70    GT:AD:DP:GQ:PL    ./.    ./.    1/1:52,38:86:18:179,18,0    ./.
chr3    75787728    rs111389701    C    T    643.34    .    AC=8;AF=1.00;AN=8;DB;DP=186;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=10.21;MQ0=140;QD=3.46    GT:AD:DP:GQ:PL    1/1:0,32:32:3:28,3,0    1/1:0,23:23:9:82,9,0    1/1:0,82:82:51:503,51,0    1/1:0,49:49:6:55,6,0

I want to remove the rows where if any of the column $10,$11,$12,$13 is having ./. no genotype then I want to eliminate those rows. Sorry for the formatting, I am not being able to get the correct format. Any suggestions?

vcftools snp vcf
• 6,341 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

Thanks a lot,

I have figured it out with the below command

sed '/\.\/\./d' input.vcf > out.vcf
• 0 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

grep -vw with appropriate escaping would do it as well

• 0 views • link
updated by Ram Ram • written by fadsfadfdsafdasfdsa fadsfadfdsafdasfdsa

Why don't you use vcftools with the --phase option?

• 0 views • link
updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

2 answers

You might take a look at vawk, which is a tool from Aaron Quinlan's group and acts as an intelligent wrapper for awk on VCF.

• 0 views • link
updated by Ram Ram • written by Matt Shirley Matt Shirley

@Matt Shirley seems quite amazing tool. However I worked it out how to do the same with my vcf file and I have already put it as an answer above but seems others missed it , its a one liner to remove the missed genotypes , however thanks everyone for the other smart ways and Matt thanks for the tool, pretty useful for other stuffs I am interested in.

• 0 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

Something like

awk 'substr($10,0,3)!="./.", substr($11,0,3)!="./.", substr($12,0,3)!="./.", substr($13,0,3)!="./."'
• 0 views • link
updated by Ram Ram • written by axelwilhelm axelwilhelm

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