The current GATK version is 3.8-0
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!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
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.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

A real deletion x a false extended deletion?

brdidobrdido São Paulo - BrazilMember

Hello again,

please, we need help understanding a deletion detected by HC.

Here is the VCF line and the activeRegions output (attached):

MT 9190 . CTGCACGACAACACAT C 1057.73 VQSRTrancheBOTH99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.935;ClippingRankSum=-0.516;DP=301;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.84;MQ0=0;MQRankSum=1.456;NEGATIVE_TRAIN_SITE;QD=0.23;ReadPosRankSum=0.625;VQSLOD=-1.682e+00;culprit=MQ;set=variant23 GT:AD:GQ:PL 0/1:51,11:99:1095,0,1411

As we can see in the image several reads confirm a 2bp deletion at 9204. But HC called a 16bp deletion (that was later on filtered out of our pipeline because of VQSR not passing our filter) that is supported only by one read. Those "Insertions" marked at the end of the reads are "N"s from masked adaptors.

I'm glad that HC tried to identify a bigger deletion, but shouldn't it call the 2bp deletion as well?

Thanks in advance,


Best Answer


Sign In or Register to comment.