Question: For multisample VCF, should I filter the variants based on allele depth (AD) or Overall depth ?
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gravatar for bioinforesearchquestions
3.4 years ago by
United States
bioinforesearchquestions270 wrote:

Hi All,

For the below vcf record, first sample is G/G (1/1-Heterozygous alternate) with allele depth of 101 reads. Whereas for the second sample is also G/G(1/1) with allele depth of 1 read. Overall depth is 102. If I filter vcf records base on DP >10. Then I will get this vcf record. But the second sample has only one 1 supporting read.

1) For multisample VCF, should I filter the variants based on allele depth (AD) or Overall depth (DP)?

2) What is VQSRTrancheBOTH99.00to99.90 (it is present in filter column)?

enter image description here

depth variants snps vcfs dnaseq • 1.3k views
ADD COMMENTlink modified 3.4 years ago by anp375170 • written 3.4 years ago by bioinforesearchquestions270
1
gravatar for anp375
3.4 years ago by
anp375170
anp375170 wrote:

if you used VQSR, correctly, you shouldn't need to filter anymore. Other than that, read about GATK's variant filtration. Their defaults are usually good.

ADD COMMENTlink written 3.4 years ago by anp375170

Thanks, anp375 for your answer.

ADD REPLYlink written 3.4 years ago by bioinforesearchquestions270
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