Question: Evaluate the sensitivity and specificity of vcf files
0
gravatar for jackycsie
4 weeks ago by
jackycsie0
jackycsie0 wrote:

Hi,

I have already finished the variant call of NA12878.

My steps are as follows:

  1. bwa mem
  2. SortSamSpark
  3. MarkDuplicatesSpark
  4. BaseRecalibratorSpark
  5. ApplyBQSRSpark
  6. HaplotypeCaller

Now I have a vcf file, but I don't know how to judge his correctness.

My reference data is:

  1. dbsnp_138.b37.vcf.
  2. Mills_and_1000G_gold_standard.indels.b37.vcf
  3. 1000G_phase1.indels.b37.vcf

Thank you, jacky.

gene • 79 views
ADD COMMENTlink modified 29 days ago • written 4 weeks ago by jackycsie0

Hi,

I find this url:

https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/

It's right or only provide chromosome 1 ?

Thanks, Jacky.

ADD REPLYlink written 29 days ago by jackycsie0

I think this is better suited for the GATK forums. There's this post that might be a good starting point: https://gatkforums.broadinstitute.org/gatk/discussion/6308/evaluating-the-quality-of-a-variant-callset

ADD REPLYlink written 28 days ago by Amar620
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