Question: Filtering vcf file by DP
0
gravatar for vskale135
4.4 years ago by
vskale13510
United Kingdom
vskale13510 wrote:

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

 

 

sequencing filtering snp vcf • 2.3k views
ADD COMMENTlink modified 4.4 years ago by Pierre Lindenbaum116k • written 4.4 years ago by vskale13510
1
gravatar for Pierre Lindenbaum
4.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

Use

* GATK/VariantFiltration http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.html#--filterExpression

* my tool vcffilterjs https://github.com/lindenb/jvarkit/wiki/VCFFilterJS

* vcftools + '--minDP'

* ...

ADD COMMENTlink written 4.4 years ago by Pierre Lindenbaum116k

Thank you Pierre..

I will check these

Sandip

ADD REPLYlink written 4.4 years ago by vskale13510
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 877 users visited in the last hour