The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

#### ☞ Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ` ) each to make a code block.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# Exclude moltype cDNA from dbSNP137

Member Posts: 39

Hi!
Since dbSNP (for humans) has a lot of variants one could question if actually are real, especially those from cDNA (mRNA), how can I ignore all SNPs in dbSNP 137 with the moltype "cDNA"?

Im asking because a lot of these SNPs may actually be RNA editing artifacts, correct?

Tagged:

• Member Posts: 39

Good, Ill try that one and post the solution when I figure it out.

• Member Posts: 39

I give up, I have to ask. I have opened the dbsnp_137.hg19.vcf file from your server and looked for anything that gives info about cDNA origin.. I cant find anything. I also tried to find other vcf from other places or something equal that had an info field about cDNA, no luck.

Any help on this?

Ah, from your question I had assumed you had a VCF with that annotation; we don't have it in ours. If there's nothing in dbSNP to that effect, then I'm afraid you're out of luck, sorry.

Geraldine Van der Auwera, PhD

• Member Posts: 39

Got it!

UCSC browser:

Go to tables -> group: variation and repeats, track: all SNPS (137) or the new 138..

There’s a field for each snp called molType. Use the list of SNPs that have a molType of "genomic" and a class of "single".