Question: ANNOVAR galaxy returning an empty file
gravatar for jaime.manion
2.0 years ago by
jaime.manion10 wrote:

I am working through a project that requires me to Identify genes with polymorphic sites using ANNOVAR annotate VCF tool. I keep getting an empty file. The previous work up is as follows and I am including a link to my process. If anyone has any insight I would really be grateful. I have checked out the previous threads and have not found a fix as my vcf file id associated with hg19.

  1. Input FASQC files for father, mother, kid
  2. Use FASQC to check for quality
  3. Use BWA to map sequences to ref genome (note 125 bp reads)
  4. AddOrReplaceRead Groups..I know that this can can cause some downstream problems my info as a sample: Input Parameter Value Note for rerun Select SAM/BAM dataset or dataset collection 132: Map with BWA-MEM on data 129 and data 128 (mapped reads in BAM format) Auto-assign false
    Read group identifier (ID) Kid Auto-assign false
    Read group sample name (SM) Kid Auto-assign false
    Library name (LB) Kid Platform/technology used to produce the reads (PL) ILLUMINA
    Platform unit (PU) Kid Sequencing center that produced the read (CN) Empty.
    Description (DS) Empty.
    Predicted median insert size (PI) Not available.
    Date that run was produced (DT) Empty.
    Select validation stringency Lenient
  5. MergeSamFiles: Used father, mother and kid
  6. filter: Removed low quality mapping, marked duplicates, CleanSam
  7. Identified polymorphic sites using FreeBayes on hg19
  8. Filtered out False Positives using VCFfilter -f "QUAL > 40" to insure sites selected where the chance of a false positive was 1 in 10K or better
  9. Extracted the workflow as VCF
  10. Reloaded the VCF file
    1. Used the VCF filter to ID: snps, Ins and Del, mnps, variants with multiple alt alleles
  11. STUCK ON using ANNOVAR on my orig. VCF file from step 10 to annotate the VCF Input Parameter Value Note for rerun Variants 155: VCFfilter: on data 142 Gene Annotations refGene gencodeV19
    Annotation Regions genomicSuperDups phastConsElements46way Annotation Databases 1000g2012apr_all avsift snp137NonFlagged esp6500si_all snp137
    Output data type VCF


annovar galaxy • 1.1k views
ADD COMMENTlink modified 19 months ago by deepti1rao10 • written 2.0 years ago by jaime.manion10
gravatar for jaime.manion
2.0 years ago by
jaime.manion10 wrote:

I needed to set the output to tabular!

ADD COMMENTlink written 2.0 years ago by jaime.manion10

Glad this worked out and thanks for taking the time to post the resolution! Jen, Galaxy team

ADD REPLYlink written 2.0 years ago by Jennifer Hillman Jackson25k
gravatar for deepti1rao
19 months ago by
deepti1rao10 wrote:

This is still not working for me, though I changed the output to tabular.

ADD COMMENTlink written 19 months ago by deepti1rao10
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