Question: ANNOVAR galaxy returning an empty file
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jaime.manion • 10 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.
https://usegalaxy.org/u/jem-r-m/h/polymorphic-sites-3-indiv
- Input FASQC files for father, mother, kid
- Use FASQC to check for quality
- Use BWA to map sequences to ref genome (note 125 bp reads)
- 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 - MergeSamFiles: Used father, mother and kid
- filter: Removed low quality mapping, marked duplicates, CleanSam
- Identified polymorphic sites using FreeBayes on hg19
- 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
- Extracted the workflow as VCF
- Reloaded the VCF file
- Used the VCF filter to ID: snps, Ins and Del, mnps, variants with multiple alt alleles
- 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
PLEASE HELP
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modified 19 months ago
by
deepti1rao • 10
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written
2.0 years ago by
jaime.manion • 10
