GATK DP filter for multiple samples
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Entering edit mode
8.0 years ago
sun.nation ▴ 140

I used GATK to call SNPs and filter based on DP < 10. I did get SNPs but having problems to get filtered SNPs.

Command to filter SNPs:

$java -jar $gatk \
   -T VariantFiltration \
   -R Corca1_AssemblyScaffolds.fa \
   -o snpsDPlt10.vcf \
   --variant snps.vcf \
   --genotypeFilterExpression "DP < 10" \
   --genotypeFilterName "DP-lt10" \
   --setFilteredGtToNocall

$java -jar $gatk \
   -T SelectVariants \
   -R Corca1_AssemblyScaffolds.fa \
   -V snpsDPlt10.vcf  \
   -o snpsDPlt10-noCall.vcf \
   --setFilteredGtToNocall

$java -jar $gatk \
   -T SelectVariants \
   -R Corca1_AssemblyScaffolds.fa \
   -V snpsDPlt10-noCall.vcf  \
   -o snpsDPlt10-final-lt10DP.vcf \
   --excludeNonVariants

Final VCF file has annotated SNPs, how can I get SNPs with DP>10:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  cotton3.fastq_1.paired.trimmed  cotton4.fastq_1.paired.trimmed
scaffold_1      67871   .       G       A       485.77  PASS    AC=1;AF=1.00;AN=1;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=
60.00;MQ0=0;QD=32.77;SOR=1.609  GT:AD:DP:FT:GQ:PL       ./.:0,3:3:DP-lt10:99:118,0      1:0,10:10:PASS:99:396,0
scaffold_1      67878   .       T       A       485.77  PASS    AC=1;AF=1.00;AN=1;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=
60.00;MQ0=0;QD=30.77;SOR=1.609  GT:AD:DP:FT:GQ:PL       ./.:0,3:3:DP-lt10:99:122,0      1:0,10:10:PASS:99:392,0
gatk snps • 3.8k views
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I have exactly the same question about DP filter. Did you find some way to filter it?

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$ bcftools view -i 'FORMAT/DP>10' input.vcf > output.vcf Or do I misunderstood something? This command will create output.vcf which contains only variants where the read depth for sample is greater 10.

fin swimmer

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