Filtering vcf file by DP

Question

[vskale135]

Hello All,

I would like to filter a vcf file based on 'DP' >= 3 field.

for example: from the following two SNPs, I would like to remove second one having DP= 1.

CcLG07  282     .       T       G       333.30  .       AC=2;AF=0.053;AN=2;BaseQRankSum=0.890;DP=199;Dels=0.00;FS=0.000;HaplotypeScore=0.6747;InbreedingCoeff=0.8342;MLEAC=2;MLEAF=0.053;MQ0=3;MQ=40.41;MQRankSum=0.564;QD=33.33;ReadPosRankSum=-1.857;VariantType=SNP  GT:AD:DP:GQ:PL  1/1:0,10:**10:**30:385,30,0
CcLG07  16686   .       T       A       82.07   .       AC=2;AF=0.333;AN=2;BaseQRankSum=-0.701;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=3.4857;InbreedingCoeff=0.3515;MLEAC=7;MLEAF=0.292;MQ0=4;MQ=24.96;MQRankSum=1.443;QD=20.52;ReadPosRankSum=-2.351;VariantType=SNP  GT:AD:DP:GQ:PL  1/1:0,1:**1**:3:29,3,0

Is there any AWK/grep command available for the same

With best

Sandip

Answer 1

[Pierre Lindenbaum]

Use

• GATK/VariantFiltration
• my tool vcffilterjs
• vcftools + --minDP
• ...

[vskale135]

Thank you Pierre..

I will check these

Sandip